Global Variome shared LOVD
COL1A2 (collagen type I alpha 2 chain)
LOVD v.3.0 Build 29 [
Current LOVD status
]
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Curators:
Gerard Pals
,
Sonna Stolk
,
Raymond Dalgleish
, and
Dimitra Micha
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Osteogenesis Imperfecta Variant Database
BMP1 (bone morphogenetic protein 1)
CCDC134 (coiled-coil domain containing 134)
COL1A1 (collagen type I alpha 1 chain)
COL1A2 (collagen type I alpha 2 chain)
CREB3L1 (cAMP responsive element binding protein 3 like 1)
CRTAP (cartilage associated protein)
FAM46A/TENT5A (family with sequence similarity 46 member A)
FKBP10 (FKBP prolyl isomerase 10)
IFITM5 (interferon induced transmembrane protein 5)
KDELR2 (KDEL endoplasmic reticulum protein retention receptor 2)
LRP5 (LDL receptor related protein 5)
MBTPS2 (membrane bound transcription factor peptidase, site 2)
MESDC2/MESD (mesoderm development candidate 2)
P3H1 (prolyl 3-hydroxylase 1)
P4HB (prolyl 4-hydroxylase subunit beta)
PLOD2 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 2)
PLS3 (plastin 3)
PPIB (peptidylprolyl isomerase B)
SEC24D (SEC24 homolog D, COPII coat complex component)
SERPINF1 (serpin family F member 1)
SERPINH1 (serpin family H member 1)
SP7 (Sp7 transcription factor)
SPARC (secreted protein acidic and cysteine rich)
TMEM38B (transmembrane protein 38B)
WNT1 (Wnt family member 1)
ADAMTS2 (ADAM metallopeptidase with thrombospondin type 1 motif 2)
AEBP1 (AE binding protein 1)
B3GALT6 (beta-1,3-galactosyltransferase 6)
B4GALT7 (beta-1,4-galactosyltransferase 7)
C1R (complement component 1, r subcomponent)
C1S (complement component 1, s subcomponent)
CHST14 (carbohydrate sulfotransferase 14)
COL1A1 (collagen type I alpha 1 chain)
COL1A2 (collagen type I alpha 2 chain)
COL3A1 (collagen type III alpha 1 chain)
COL5A1 (collagen type V alpha 1 chain)
COL5A2 (collagen type V alpha 2 chain)
DSE (dermatan sulfate epimerase)
FKBP14 (FKBP prolyl isomerase 14)
PLOD1 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 1)
PLOD3 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 3)
TNXB (tenascin XB)
The variants shown are described using the NM_000089.3 transcript reference sequence.
Legend
Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.
Effect
: The variant's effect on the function of the gene/protein, displayed in the format 'R/C'. R is the value reported by the source (publication, submitter) and this classification may vary between records. C is the value concluded by the curator. Note that in some database the curator uses Summary records to give details on the classification of the variant.Values used: '+' indicating the variant affects function, '+?' probably affects function, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect was not classified.
Exon
: number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = from intron 2 to intron 7, 8i_9 = intron 8/exon 9 boundary, _1 = 5' to exon 1, 18_ = 3' of exon 18, _1_18_ = encompassing the entire 18-exon gene
DNA change (cDNA)
: description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup. For deletions/duplications extending beyond the reference transcript resp. {0}/{2} is used to replace del/dup. Extent of the deletion/duplication should be specified using the genomic description (g.). "-" indicates the variant described on genomic level does not affect the coding DNA reference sequence.
RNA change
: description of variant at RNA level (following HGVS recommendations).
r.123c>u
r.? = unknown
r.(?) = RNA not analysed but probably transcribed copy of DNA variant
r.spl? = RNA not analysed but variant probably affects splicing
r.(spl?) = RNA not analysed but variant may affect splicing
r.0? = change expected to abolish transcription
Protein
: description of variant at protein level (following HGVS recommendations).
p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
p.Arg345Pro = change derived from RNA analysis
p.? = unknown effect
p.0? = probably no protein produced
Predicted
: predicted consequence of variant (RNA/protein level)
All options:
missense
nonsense
frameshift
no-stop
silent
splicing affected
splicing affected, exon skipped
splicing affected?
deletion
deletion, small
deletion, large
deletion, exon
deletion, multi exon
duplication
duplication, small
duplication, large
insertion
insertion, small
insertion, large
delins = insertion/deletion
conversion
other/complex
Legacy protein change
: description of variant at protein level using a traditional (legacy) numbering system.
Allele
: On which allele is the variant located? Does not necessarily imply inheritance! 'Paternal' (confirmed or inferred), 'Maternal' (confirmed or inferred), 'Parent #1' or #2 for compound heterozygosity without having screened the parents, 'Unknown' for heterozygosity without having screened the parents, 'Both' for homozygozity.
Classification method
: The method used for the clinical classification of this variant.
All options:
ACMG
ACGS
EAHAD-CFDB
ENIGMA
IARC
InSiGHT
kConFab
other
Clinical classification
: Clinical classification of variant, preferably based on standardised criteria (e.g. ACMG), directed on the clinical consequences as published/submitted, indicated using an enriched system including inheritance: e.g. pathogenic, pathogenic (dominant), pathogenic (recessive), pathogenic (!), pathogenic (maternal), pathogenic (paternal). Standard inheritance is covered by dominant/recessive, imprinting by maternal/paternal. A '!' warns for exceptional circumstances to be explained in the 'Remarks' field (low penetrance, variants pathogenic in heterozygous state only, hypomorphic/hypermorphic variants, protective variants, etc.). Non-disease consequences (e.g. drug metabolism (pharmacogenetics), risk factor, blood group, tasting bitter) are indicated using additions to the benign classification; benign (dominant), benign (recessive), benign (!), etc. The value 'association' is used for variants associated with a phenotype and 'NA' for variants from in vitro/in silico records. NOTE: classification may differ from the opinion of the curator as given in a variant SUMMARY-record or the 'Functional effect concluded'). NOTE: pathogenic/likely pathogenic should go together with "variant (probably) affects function" In ClassFunctional.
All options:
pathogenic
pathogenic (dominant)
pathogenic (recessive)
pathogenic (!)
pathogenic (maternal)
pathogenic (paternal)
likely pathogenic
likely pathogenic (dominant)
likely pathogenic (recessive)
likely pathogenic (!)
likely pathogenic (maternal)
likely pathogenic (paternal)
VUS
VUS (!)
likely benign
likely benign (dominant)
likely benign (recessive)
likely benign (!)
likely benign (maternal)
likely benign (paternal)
benign
benign (dominant)
benign (recessive)
benign (!)
benign (maternal)
benign (paternal)
association
unclassified
NA
DNA change (genomic) (hg19)
: HGVS description of variant at DNA level, based on the genomic (chromosomal) DNA reference sequence; e.g. g.12345678C>T, g.12345679del, g.12345678_12345890dup
DNA change (hg38)
: HGVS description of variant at DNA level, based on the hg38 genomic (chromosomal) eference sequence; e.g. g.12345678C>T, g.12345679del, g.12345678_12345890dup
Published as
: listed only when different from "DNA change"; variant as reported originally (e.g. 521delT). Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G)
ISCN
: description of the variant according to ISCN nomenclature
DB-ID
: database ID of variant, grouping multiple observations of the same variant together, starting with the HGNC gene symbol, followed by an underscore (_) and a six digit number (e.g. DMD_012345). _000000 is used for variants where DNA was not analysed (change predicted from RNA analysis), variants seen in animal models or variants not seen in humans but functionally tested in vitro
Variant remarks
: remarks regarding variant described, e.g. germline mosaicism in mother, 345 kb deletion, muscle RNA analysed, not in 200 control chromosomes tested, on founder haplotype, etc.
Reference
: publication describing the variant submitted, incl. links to OMIM, PubMed or other source, e.g. "den Dunnen ASHG2003 P2346"
ClinVar ID
: ID of variant in ClinVar database
dbSNP ID
: the dbSNP ID
Origin
: Origin of variant/record: Germline = in all cells, De novo = in all cells, but not in either parent, Germline/De novo (untested) = in all cells, parents not tested (use only when De novo is likely, e.g. isolated/sporadic cases with dominant disease), Somatic = present in a subset of cells, but not in either parent, Uniparental disomy = from parental disomy (maternal or paternal), CLASSIFICATION record = submitter only sharing variant classification (note another report may share Individual data), SUMMARY record = master summary record from curator (may link to another database), In vitro (cloned) = data resulting from in vitro functional assays, animal model = data from animal model, Artefact = false positive variant call, DUPLICATE record = variant already described on another chromosome (e.g. unbalanced translocation, duplicating transposition, 2nd fusion transcript, etc.)
All options:
Germline
De novo
Germline/De novo (untested)
Somatic
Uniparental disomy
Uniparental disomy, maternal allele
Uniparental disomy, paternal allele
CLASSIFICATION record
SUMMARY record
In vitro (cloned)
In silico
animal model
Artefact
DUPLICATE record
Unknown
Not applicable
Segregation
: Indicates whether the variant segregates with the phenotype (yes), does not segregate with the phenotype (no) or segregation is unknown (?)
All options:
? = unknown
yes = segregates with phenotype
no = does not segregate with phenotype
- = not applicable
Frequency
: frequency in which the variant was found; e.g 5/760 chromosomes (in 5 of 760 chromosomes tested), 1/33 patients (in 1 of 33 patients analysed in study), 0.05 controls (in 5% of control cases tested)
Re-site
: restriction enzyme recognition site created (+) or destroyed (-); e.g. BglII+;BamHI-
VIP
: variant VIP-status was requested for matchmaking - need collaboration(s) to crack the case - please contact the submitter/curator. NOTE: to get VIP status ask the curator.
Methylation
: result of methylation test; GOM (gain of methylation), LOM (loss of methylation), 30% (30% methylated). NOTE: when several tests were done mention the method as well (e.g. MS-PCR 75%)
Template
: Template(s) used to detect the sequence variant; DNA (genomic DNA), RNA (cDNA) or protein
All options:
DNA
RNA = RNA (cDNA)
protein
? = unknown
Technique
: technique(s) used to identify the sequence variant.
All options:
? = unknown
ARMS = amplification refractory mutation system
arrayCGH = array for Comparative Genomic Hybridisation
arraySEQ = array for resequencing
arraySNP = array for SNP typing
arrayCNV = array for Copy Number Variation (SNP and CNV probes)
ASO = allele-specific oligo hybridisation
BESS = Base Excision Sequence Scanning
CMC = Chemical Mismatch Cleavage
COBRA = Combined Bisulfite Restriction Analysis
CSCE = Conformation Sensitive Capillary Electrophoresis
CSGE = Conformation Sensitive Gel Electrophoresis
ddF = dideoxy Fingerprinting
DGGE = Denaturing-Gradient Gel-Electrophoresis
DHPLC = Denaturing High-Performance Liquid Chromatography
DOVAM = Detection Of Virtually All Mutations (SSCA variant)
DSCA = Double-Strand DNA Conformation Analysis
DSDI = Detection Small Deletions and Insertions
EMC = Enzymatic Mismatch Cleavage
expr = expression analysis
FISH = Fluorescent In-Situ Hybridisation
FISHf = fiberFISH
HD = HeteroDuplex analysis
HPLC = High-Performance Liquid Chromatography
IEF = IsoElectric Focussing
IHC = Immuno-Histo-Chemistry
Invader = Invader assay
MAPH = Multiplex Amplifiable Probe Hybridisation
MAQ = Multiplex Amplicon Quantification
MCA = Melting Curve Analysis, high-resolution (HRMA)
microscope = microscopic analysis (karyotype)
microsat = microsatellite genotyping
minigene = expression minigene construct
MIP = Molecular Inversion Probe amplification
MIPsm = singele molecule Molecular Inversion Probe amplification
MLPA = Multiplex Ligation-dependent Probe Amplification
MLPA-ms = Multiplex Ligation-dependent Probe Amplification, methylation specific
MS = mass spectrometry
Northern = Northern blotting
NUC = nuclease digestion (RNAseT1, S1)
OM = optical mapping
PAGE = Poly-Acrylamide Gel-Electrophoresis
PCR = Polymerase Chain Reaction
PCRdd = PCR, digital droplet
PCRdig = PCR + restriction enzyme digestion
PCRh = PCR, haloplex
PCRlr = PCR, long-range
PCRm = PCR, multiplex
PCRms = PCR, methylation sensitive
PCRq = PCR, quantitative (qPCR)
PCRrp = PCR, repeat-primed (RP-PCR)
PCRsqd = PCR, semi-quantitative duplex
PE = primer extension (APEX, SNaPshot)
PEms = primer extension, methylation-sensitive single-nucleotide
PFGE = Pulsed-Field Gel-Electrophoresis (+Southern)
PTT = Protein Truncation Test
RFLP = Restriction Fragment Length Polymorphisms
RT-PCR = Reverse Transcription and PCR
RT-PCRq = Reverse Transcription and PCR, quantitative
SBE = Single Base Extension
SEQ = SEQuencing (Sanger)
SEQb = bisulfite SEQuencing
SEQp = pyroSequencing
SEQms = sequencing, methylation specific
SEQ-ON = next-generation sequencing - Oxford Nanopore
SEQ-NG = next-generation sequencing
SEQ-NG-RNA = next-generation sequencing RNA
SEQ-NG-H = next-generation sequencing - Helicos
SEQ-NG-I = next-generation sequencing - Illumina/Solexa
SEQ-NG-IT = next-generation sequencing - Ion Torrent
SEQ-NG-R = next-generation sequencing - Roche/454
SEQ-NG-S = next-generation sequencing - SOLiD
SEQ-PB = next-generation sequencing - Pacific Biosciences
SNPlex = SNPlex
Southern = Southern blotting
SSCA = Single-Strand DNA Conformation polymorphism Analysis (SSCP)
SSCAf = fluorescent SSCA (SSCP)
STR = Short Tandem Repeat
TaqMan = TaqMan assay
Western = Western blotting
- = not applicable
Tissue
: tissue type used for analysis
Remarks
: remarks regarding the screening like WGS (whole genome sequencing), WES (whole exome sequencing, gene panel (incl. a list of genes analysed), etc.
ID_report
: ID of the individual that can be publically shared, e.g. as listed in a publication
Reference
: reference to publication describing the individual/family, possibly giving more phenotypic details than listed in this database entry, incl. link to PubMed or other source, e.g. "den Dunnen ASHG2003 P2346"
Remarks
: remarks about the individual
Gender
: gender individual
All options:
? = unknown
- = not applicable
F = female
M = male
rF = raised as female
rM = raised as male
Consanguinity
: indicates whether the parents are related (consanguineous), not related (non-consanguineous) or whether consanguinity is not known (unknown)
All options:
no = non-consanguineous parents
yes = consanguineous parents
likely = consanguinity likely
? = unknown
- = not applicable
Country
: where (country) does the individual live/recently came from. Give additional details (population, specific sub-group) and when parents come from different countries in "Population". Belgium = individual lives in/recently came from Belgium, (France) = reported by laboratory in France, individual's country of origin not sure
All options:
? (unknown)
- (not applicable)
Afghanistan
(Afghanistan)
Albania
(Albania)
Algeria
(Algeria)
American Samoa
(American Samoa)
Andorra
(Andorra)
Angola
(Angola)
Anguilla
(Anguilla)
Antarctica
(Antarctica)
Antigua and Barbuda
(Antigua and Barbuda)
Argentina
(Argentina)
Armenia
(Armenia)
Aruba
(Aruba)
Australia
(Australia)
Austria
(Austria)
Azerbaijan
(Azerbaijan)
Bahamas
(Bahamas)
Bahrain
(Bahrain)
Bangladesh
(Bangladesh)
Barbados
(Barbados)
Belarus
(Belarus)
Belgium
(Belgium)
Belize
(Belize)
Benin
(Benin)
Bermuda
(Bermuda)
Bhutan
(Bhutan)
Bolivia
(Bolivia)
Bosnia and Herzegovina
(Bosnia and Herzegovina)
Botswana
(Botswana)
Bouvet Island
(Bouvet Island)
Brazil
(Brazil)
British Indian Ocean Territory
(British Indian Ocean Territory)
Brunei Darussalam
(Brunei Darussalam)
Bulgaria
(Bulgaria)
Burkina Faso
(Burkina Faso)
Burundi
(Burundi)
Cambodia
(Cambodia)
Cameroon
(Cameroon)
Canada
(Canada)
Cape Verde
(Cape Verde)
Cayman Islands
(Cayman Islands)
Central African Republic
(Central African Republic)
Central Europe
Chad
(Chad)
Chile
(Chile)
China
(China)
Christmas Island
(Christmas Island)
Cocos (Keeling Islands)
(Cocos (Keeling Islands))
Colombia
(Colombia)
Comoros
(Comoros)
Congo
(Congo)
Cook Islands
(Cook Islands)
Costa Rica
(Costa Rica)
Cote D'Ivoire (Ivory Coast)
(Cote D'Ivoire (Ivory Coast))
Croatia (Hrvatska)
(Croatia (Hrvatska))
Cuba
(Cuba)
Cyprus
(Cyprus)
Czech Republic
(Czech Republic)
Denmark
(Denmark)
Djibouti
(Djibouti)
Dominica
(Dominica)
Dominican Republic
(Dominican Republic)
East Timor
(East Timor)
Ecuador
(Ecuador)
Egypt
(Egypt)
El Salvador
(El Salvador)
England
(England)
Equatorial Guinea
(Equatorial Guinea)
Eritrea
(Eritrea)
Estonia
(Estonia)
Ethiopia
(Ethiopia)
Falkland Islands (Malvinas)
(Falkland Islands (Malvinas))
Faroe Islands
(Faroe Islands)
Fiji
(Fiji)
Finland
(Finland)
France
(France)
Gabon
(Gabon)
Gambia
(Gambia)
Georgia
(Georgia)
Germany
(Germany)
Ghana
(Ghana)
Gibraltar
(Gibraltar)
Greece
(Greece)
Greenland
(Greenland)
Grenada
(Grenada)
Guadeloupe
(Guadeloupe)
Guam
(Guam)
Guatemala
(Guatemala)
Guiana, French
(Guiana, French)
Guinea
(Guinea)
Guinea-Bissau
(Guinea-Bissau)
Guyana
(Guyana)
Haiti
(Haiti)
Heard and McDonald Islands
(Heard and McDonald Islands)
Honduras
(Honduras)
Hong Kong
(Hong Kong)
Hungary
(Hungary)
Iceland
(Iceland)
India
(India)
Indonesia
(Indonesia)
Iran
(Iran)
Iraq
(Iraq)
Ireland
(Ireland)
Israel
(Israel)
Italy
(Italy)
Jamaica
(Jamaica)
Japan
(Japan)
Jordan
(Jordan)
Kazakhstan
(Kazakhstan)
Kenya
(Kenya)
Kiribati
(Kiribati)
Korea
(Korea)
Korea, North (People's Republic)
(Korea, North (People's Republic))
Korea, South (Republic)
(Korea, South (Republic))
Kosovo
(Kosovo)
Kuwait
(Kuwait)
Kyrgyzstan (Kyrgyz Republic)
(Kyrgyzstan (Kyrgyz Republic))
Laos
(Laos)
Latvia
(Latvia)
Lebanon
(Lebanon)
Lesotho
(Lesotho)
Liberia
(Liberia)
Libya
(Libya)
Liechtenstein
(Liechtenstein)
Lithuania
(Lithuania)
Luxembourg
(Luxembourg)
Macau
(Macau)
Macedonia
(Macedonia)
Madagascar
(Madagascar)
Malawi
(Malawi)
Malaysia
(Malaysia)
Maldives
(Maldives)
Mali
(Mali)
Mallorca
(Mallorca)
Malta
(Malta)
Marshall Islands
(Marshall Islands)
Martinique
(Martinique)
Mauritania
(Mauritania)
Mauritius
(Mauritius)
Mayotte
(Mayotte)
Mexico
(Mexico)
Micronesia
(Micronesia)
Moldova
(Moldova)
Monaco
(Monaco)
Mongolia
(Mongolia)
Montserrat
(Montserrat)
Morocco
(Morocco)
Mozambique
(Mozambique)
Myanmar
(Myanmar)
Namibia
(Namibia)
Nauru
(Nauru)
Nepal
(Nepal)
Netherlands
(Netherlands)
Netherlands Antilles
(Netherlands Antilles)
Neutral Zone (Saudia Arabia/Iraq)
(Neutral Zone (Saudia Arabia/Iraq))
New Caledonia
(New Caledonia)
New Zealand
(New Zealand)
Nicaragua
(Nicaragua)
Niger
(Niger)
Nigeria
(Nigeria)
Niue
(Niue)
Norfolk Island
(Norfolk Island)
Northern Ireland
(Northern Ireland)
Northern Mariana Islands
(Northern Mariana Islands)
Norway
(Norway)
Oman
(Oman)
Pakistan
(Pakistan)
Palau
(Palau)
Palestine
(Palestine)
Panama
(Panama)
Papua New Guinea
(Papua New Guinea)
Paraguay
(Paraguay)
Peru
(Peru)
Philippines
(Philippines)
Pitcairn
(Pitcairn)
Poland
(Poland)
Polynesia, French
(Polynesia, French)
Portugal
(Portugal)
Puerto Rico
(Puerto Rico)
Qatar
(Qatar)
Reunion
(Reunion)
Romania
(Romania)
Russia
(Russia)
Russian Federation
(Russian Federation)
Rwanda
(Rwanda)
S. Georgia and S. Sandwich Isls.
(S. Georgia and S. Sandwich Isls.)
Saint Kitts and Nevis
(Saint Kitts and Nevis)
Saint Lucia
(Saint Lucia)
Saint Vincent and The Grenadines
(Saint Vincent and The Grenadines)
Samoa
(Samoa)
San Marino
(San Marino)
Sao Tome and Principe
(Sao Tome and Principe)
Saudi Arabia
(Saudi Arabia)
Scotland
(Scotland)
Senegal
(Senegal)
Serbia
(Serbia)
Seychelles
(Seychelles)
Sierra Leone
(Sierra Leone)
Singapore
(Singapore)
Slovakia (Slovak Republic)
(Slovakia (Slovak Republic))
Slovenia
(Slovenia)
Solomon Islands
(Solomon Islands)
Somalia
(Somalia)
South Africa
(South Africa)
Southern Territories, French
(Southern Territories, French)
Soviet Union (former)
(Soviet Union (former))
Spain
(Spain)
Sri Lanka
(Sri Lanka)
St. Helena, Ascension and Tristan da
Cunha
(St. Helena, Ascension and Tristan da
Cunha)
St. Pierre and Miquelon
(St. Pierre and Miquelon)
Sudan
(Sudan)
Sudan, South
(Sudan, South)
Suriname
(Suriname)
Svalbard and Jan Mayen Islands
(Svalbard and Jan Mayen Islands)
Swaziland
(Swaziland)
Sweden
(Sweden)
Switzerland
(Switzerland)
Syria
(Syria)
Taiwan
(Taiwan)
Tajikistan
(Tajikistan)
Tanzania
(Tanzania)
Thailand
(Thailand)
Togo
(Togo)
Tokelau
(Tokelau)
Tonga
(Tonga)
Trinidad and Tobago
(Trinidad and Tobago)
Tunisia
(Tunisia)
Turkey
(Turkey)
Turkmenistan
(Turkmenistan)
Turks and Caicos Islands
(Turks and Caicos Islands)
Tuvalu
(Tuvalu)
Uganda
(Uganda)
Ukraine
(Ukraine)
United Arab Emirates
(United Arab Emirates)
United Kingdom (Great Britain)
(United Kingdom (Great Britain))
United States
(United States)
Uruguay
(Uruguay)
US Minor Outlying Islands
(US Minor Outlying Islands)
Uzbekistan
(Uzbekistan)
Vanuatu
(Vanuatu)
Vatican City State (Holy See)
(Vatican City State (Holy See))
Venezuela
(Venezuela)
Viet Nam
(Viet Nam)
Virgin Islands (British)
(Virgin Islands (British))
Virgin Islands (US)
(Virgin Islands (US))
Wales
(Wales)
Wallis and Futuna Islands
(Wallis and Futuna Islands)
Western Sahara
(Western Sahara)
Yemen
(Yemen)
Yugoslavia
(Yugoslavia)
Zaire
(Zaire)
Zambia
(Zambia)
Zimbabwe
(Zimbabwe)
Population
: population the individual (or ancestors) belongs to; e.g. white, gypsy, Jewish-Ashkenazi, Africa-N, Sardinia, etc.
Age at death
: age at which the individual deceased (when applicable):
35y = 35 years
>43y = still alive at 43y
04y08m = 4 years and 8 months
00y00m01d12h = 1 day and 12 hours
18y? = around 18 years
30y-40y = between 30 and 40 years
>54y = older than 54
? = unknown
VIP
: individual/phenotype VIP-status was requested for matchmaking - need collaboration(s) to crack the case - please contact the submitter/curator. NOTE: to get VIP status ask the curator.
Data_av
: are additional data available upon request: e.g. pedigree (yes/no/?)
Treatment
: treatment of patient
How to query this table
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all entries containing 'South Asian', but not containing 'South East Asian'
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1663 entries on 17 pages. Showing entries 1 - 100.
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Effect
Exon
DNA change (cDNA)
RNA change
Protein
Predicted
Legacy protein change
Allele
Classification method
Clinical classification
DNA change (genomic) (hg19)
DNA change (hg38)
Published as
ISCN
DB-ID
Variant remarks
Reference
ClinVar ID
dbSNP ID
Origin
Segregation
Frequency
Re-site
VIP
Methylation
Template
Technique
Tissue
Remarks
Disease
ID_report
Reference
Remarks
Gender
Consanguinity
Country
Population
Age at death
VIP
Data_av
Treatment
Panel size
Owner
+/.
17
[NM_181678.2:c.-48-58227]::c.869del
r.?
p.?
-
-
Unknown
-
pathogenic
g.94038711_qterdelins[NC_000005.9:146294373_qter]
-
chr5:146294373,chr7:94038710
t(5;7)(q32;q21)
COL1A2_000000
translocation
PubMed: Liu 2017
-
-
Germline/De novo (untested)
-
-
-
-
-
DNA
SEQ-NG
-
targeted 14-gene panel OI
OI
Fam27
PubMed: Liu 2017
analysis 101 unrelated OI families
-
-
China
-
-
-
-
-
1
Johan den Dunnen
+/+
_1_18i
c.-471_(936+1_937-1){0}
r.0?
p.0?
deletion, multi exon
-
Unknown
-
pathogenic
g.(?_94023873)_(94038921_94039034)del
g.(?_94394561)_(94409609_94409722)del
-
-
COL1A2_000413
-
-
-
-
Unknown
-
-
-
-
-
DNA
MLPA
-
-
OI, OI4
-
-
-
-
-
-
-
-
-
-
-
1
Isabel Mandy Nesbitt
+/+
1i
c.70+717A>G
r.(?)
p.?
other/complex
-
Unknown
-
pathogenic
g.94025130A>G
-
-
-
COL1A2_000261
-
PubMed: Schwarze et al., 2004
-
rs72656354
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS
-
PubMed: Schwarze et al., 2004
Both mutations result in null alleles.
-
-
-
-
-
-
-
-
1
Peter Byers
-?/.
1i
c.71-17C>T
r.(=)
p.(=)
-
-
Unknown
-
likely benign
g.94027043C>T
g.94397731C>T
-
-
COL1A2_000698
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
1i
c.71-8_71-7dup
r.(=)
p.(=)
-
-
Unknown
-
benign
g.94027052_94027053dup
g.94397740_94397741dup
COL1A2(NM_000089.4):c.71-8_71-7dupTT
-
COL1A2_000702
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
1i
c.71-7dup
r.(=)
p.(=)
-
-
Unknown
-
benign
g.94027053dup
g.94397741dup
COL1A2(NM_000089.4):c.71-7dupT
-
COL1A2_000816
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
2i
c.81+10A>G
r.(=)
p.(=)
-
-
Unknown
-
likely benign
g.94027080A>G
g.94397768A>G
COL1A2(NM_000089.3):c.81+10A>G
-
COL1A2_000817
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
2i
c.81+11del
r.(=)
p.(=)
-
-
Unknown
-
likely benign
g.94027081del
g.94397769del
COL1A2(NM_000089.4):c.81+11delC
-
COL1A2_000818
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
2i
c.81+15T>C
r.(=)
p.(=)
-
-
Unknown
-
likely benign
g.94027085T>C
g.94397773T>C
COL1A2(NM_000089.3):c.81+15T>C, COL1A2(NM_000089.4):c.81+15T>C
-
COL1A2_000819
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
2i
c.81+15T>C
r.(=)
p.(=)
-
-
Unknown
-
likely benign
g.94027085T>C
-
COL1A2(NM_000089.3):c.81+15T>C, COL1A2(NM_000089.4):c.81+15T>C
-
COL1A2_000819
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
2i
c.82-12A>G
r.(=)
p.(=)
-
-
Unknown
-
benign
g.94027682A>G
g.94398370A>G
COL1A2(NM_000089.4):c.82-12A>G
-
COL1A2_000820
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
3
c.87T>C
r.(?)
p.(Thr29=)
-
-
Unknown
-
benign
g.94027699T>C
g.94398387T>C
COL1A2(NM_000089.4):c.87T>C (p.T29=)
-
COL1A2_000308
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/-
3
c.87T>C
r.(?)
p.(=)
silent
-
Unknown
-
likely benign
g.94027699T>C
-
-
-
COL1A2_000308
-
PubMed: Zhuang et al., 1996
PubMed: Yoneyama et al., 2004
PubMed: Chan et al., 2008
PubMed: Bodian et al., 2009
-
rs1801182
Unknown
-
-
-
-
-
DNA
PCR, SEQ
-
-
?
-
PubMed: Zhuang et al., 1996
PubMed: Yoneyama et al., 2004
PubMed: Chan et al., 2008
PubMed: Bodian et al., 2009
-
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
-?/-?
4
c.118C>A
r.(?)
p.(Pro40Thr)
missense
-
Unknown
-
benign
g.94028382C>A
-
-
-
COL1A2_000391
-
-
-
-
Unknown
-
-
-
-
-
DNA
SEQ
-
-
OI
-
-
Complete sequencing of COL1A1 and COL1A2, no other changes detected
-
-
-
-
-
-
-
-
1
Isabel Mandy Nesbitt
-/.
-
c.132+31G>A
r.(=)
p.(=)
-
-
Unknown
-
benign
g.94028427G>A
-
COL1A2(NM_000089.4):c.132+31G>A
-
COL1A2_000924
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
4i
c.133-304G>A
r.(=)
p.(=)
-
-
Unknown
-
likely benign
g.94029204G>A
-
COL1A2(NM_000089.4):c.133-304G>A
-
COL1A2_000875
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/+
5
c.133G>T
r.(?)
p.(Gly45Cys)
missense
-
Paternal (inferred)
-
pathogenic
g.94029508G>T
-
-
-
COL1A2_000757
-
Morlino et al., submitted 2019
-
-
Unknown
-
-
-
-
-
DNA
PCR, SEQ
-
-
EDS
-
Morlino et al., submitted 2019
Father of affected individual AN_005716.
-
-
-
-
-
-
-
-
1
Marina Colombi, Marco Ritelli
+?/.
-
c.152_157dup
r.(?)
p.(Gly51_Arg52dup)
-
-
Maternal (inferred)
-
likely pathogenic
g.94029527_94029532dup
g.94400215_94400220dup
-
-
COL1A2_000909
-
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
blood
-
?
-
-
-
-
-
Italy
-
-
-
-
-
1
Lucia Micale
-?/.
5
c.180C>A
r.(?)
p.(Gly60=)
-
-
Unknown
-
likely benign
g.94029555C>A
g.94400243C>A
COL1A2(NM_000089.4):c.180C>A (p.G60=)
-
COL1A2_000821
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+?/.
5
c.197G>A
r.(?)
p.(Gly66Asp)
-
-
Unknown
-
likely pathogenic
g.94029572G>A
g.94400260G>A
-
-
COL1A2_000822
-
-
-
-
Unknown
-
-
-
-
-
DNA
SEQ
-
-
EDS
Family6-P10
-
family, 2 affected
M
-
-
-
-
-
-
-
2
Lucia Micale
+?/.
5
c.197G>A
r.(?)
p.(Gly66Asp)
-
-
Unknown
-
likely pathogenic
g.94029572G>A
g.94400260G>A
-
-
COL1A2_000822
-
-
-
-
Unknown
-
-
-
-
-
DNA
SEQ
blood
-
EDS
Family6-P11
-
-
M
-
-
-
30y
-
-
-
1
Lucia Micale
+?/.
5
c.197G>A
r.(?)
p.(Gly66Asp)
-
-
Paternal (inferred)
-
likely pathogenic
g.94029572G>A
g.94400260G>A
-
-
COL1A2_000822
-
PubMed: Morlino 2020
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
blood
-
?
-
PubMed: Morlino 2020
-
-
-
Italy
-
-
-
-
-
1
Lucia Micale
+/+?
5
c.214G>A
r.(?)
p.(Gly72Ser)
missense
-
Maternal (confirmed)
-
likely pathogenic
g.94029589G>A
-
-
-
COL1A2_000513
-
-
-
-
Unknown
-
-
-
-
-
RNA
RT-PCR, SEQ
-
-
OI, OI1
-
-
-
-
-
-
Brazilian
-
-
-
-
1
Lilia D'Souza-Li
+/+
5i
c.226-22_226-11del
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030857_94030868del
-
-
-
COL1A2_000434
-
PubMed: Giunta and Steinmann, 2008
-
-
Unknown
-
-
-
-
-
?
?
-
-
EDS, EDSARTH2
-
PubMed: Giunta and Steinmann, 2008
The deletion causes skipping of exon 6. The patient's daughter also harbours the same mutation.
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/+
5i_6i
c.226-17_279+12del
r.spl
p.(Asn76_Met93del)
deletion, exon
-
Unknown
-
pathogenic
g.94030862_94030944del
-
-
-
COL1A2_000207
-
PubMed: Byers et al., 1997
-
rs74315131
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Byers et al., 1997
The mutation in this patient in terms of genomic coordinates is g.11990_12072del
-
-
-
-
-
-
-
-
1
Peter Byers
-/.
5i
c.226-11del
r.(=)
p.(=)
-
-
Unknown
-
benign
g.94030868del
g.94401556del
COL1A2(NM_000089.4):c.226-11delT
-
COL1A2_000823
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
5i
c.226-11dup
r.(=)
p.(=)
-
-
Unknown
-
benign
g.94030868dup
g.94401556dup
COL1A2(NM_000089.3):c.226-11dupT, COL1A2(NM_000089.4):c.226-11dupT
-
COL1A2_000824
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/.
-
c.226-11dup
r.(=)
p.(=)
-
-
Unknown
-
benign
g.94030868dup
-
COL1A2(NM_000089.3):c.226-11dupT, COL1A2(NM_000089.4):c.226-11dupT
-
COL1A2_000824
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
5i
c.226-10A>T
r.(=)
p.(=)
-
-
Unknown
-
likely benign
g.94030869A>T
g.94401557A>T
COL1A2(NM_000089.3):c.226-10A>T
-
COL1A2_000825
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
5i
c.226-9C>T
r.(=)
p.(=)
-
-
Unknown
-
likely benign
g.94030870C>T
g.94401558C>T
COL1A2(NM_000089.3):c.226-9C>T
-
COL1A2_000826
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-?/.
5i
c.226-6C>T
r.(=)
p.(=)
-
-
Unknown
-
likely benign
g.94030873C>T
g.94401561C>T
COL1A2(NM_000089.3):c.226-6C>T
-
COL1A2_000827
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/+
5i
c.226-2A>G
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030877A>G
-
-
-
COL1A2_000224
-
PubMed: Byers et al., 1997
-
rs72656355
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Byers et al., 1997
-
-
-
-
-
-
-
-
-
1
Peter Byers
+/+
5i
c.226-2A>G
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030877A>G
-
-
-
COL1A2_000224
-
PubMed: Marini et al., 2007
(Marini, Cabral and Pals, personal communication)
-
rs72656355
Unknown
-
-
-
-
-
?
?
-
-
EDS, EDSARTH2
-
PubMed: Marini et al., 2007
(Marini, Cabral and Pals, personal communication)
-
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/+
5i
c.226-2A>G
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030877A>G
-
-
-
COL1A2_000224
-
PubMed: Klaassens et al., 2011
-
rs72656355
Unknown
-
-
-
-
-
DNA
PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Klaassens et al., 2011
The mutation results in use of a cryptic splice site 15 bases into exon 6, resulting in the loss of the first 5 amino acids.
-
-
-
white
-
-
-
-
1
Raymond Dalgleish
+/.
-
c.226-2A>G
r.spl?
p.?
-
-
Unknown
-
pathogenic
g.94030877A>G
-
COL1A2(NM_000089.4):c.226-2A>G
-
COL1A2_000224
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/+
5i
c.226-1G>A
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030878G>A
-
-
-
COL1A2_000225
-
PubMed: Byers et al., 1997
-
rs66820119
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Byers et al., 1997
-
-
-
-
-
-
-
-
-
1
Peter Byers
+/+
5i
c.226-1G>C
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030878G>C
-
-
-
COL1A2_000226
-
PubMed: Chiodo et al., 1992
-
rs66820119
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Chiodo et al., 1992
The mutation acivates a cryptic splice acceptor in exon 6 resulting in the loss of the first 5 amino acids encoded by that exon.
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
-/.
6
c.246T>C
r.(?)
p.(Asp82=)
-
-
Unknown
-
benign
g.94030899T>C
g.94401587T>C
COL1A2(NM_000089.4):c.246T>C (p.D82=)
-
COL1A2_000309
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/-
6
c.246T>C
r.(?)
p.(=)
silent
-
Unknown
-
likely benign
g.94030899T>C
-
-
-
COL1A2_000309
-
PubMed: Strobel et al., 1992
PubMed: Yoneyama et al., 2004
PubMed: Chan et al., 2008
PubMed: Bodian et al., 2009
-
rs1800222
Unknown
-
-
-
-
-
DNA
PCR, SEQ
-
-
?
-
PubMed: Strobel et al., 1992
PubMed: Yoneyama et al., 2004
PubMed: Chan et al., 2008
PubMed: Bodian et al., 2009
-
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/+
6
c.279G>A
r.(?)
p.(Met93Ile)
splicing affected?
Met3Ile
Unknown
-
pathogenic
g.94030932G>A
-
-
-
COL1A2_000227
-
PubMed: Byers et al., 1997
-
rs72656356
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Byers et al., 1997
Skips exon 6.
-
-
-
-
-
-
-
-
1
Peter Byers
+/+
6
c.279G>A
r.(?)
p.(Met93Ile)
splicing affected?
Met3Ile
Unknown
-
pathogenic
g.94030932G>A
-
-
-
COL1A2_000227
-
PubMed: Weil et al., 1989b
-
rs72656356
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Weil et al., 1989b
Skips exon 6. The mutation was demonstrated to be temperature-sensitive in this patient.
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/+
6i
c.279+1G>A
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030933G>A
-
-
-
COL1A2_000228
-
PubMed: Weil et al., 1990
-
rs67398234
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Weil et al., 1990
Skips exon 6.
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/+
6i
c.279+1G>A
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030933G>A
-
-
-
COL1A2_000228
-
PubMed: Vasan et al., 1991
-
rs67398234
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, NUC, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Vasan et al., 1991
Skips exon 6.The technique used was S1 nuclease.
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/+
6i
c.279+1G>A
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030933G>A
-
-
-
COL1A2_000228
-
PubMed: Nicholls et al., 1991
-
rs67398234
Unknown
-
-
-
-
-
DNA, RNA
PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Nicholls et al., 1991
Skips exon 6.
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/+
6i
c.279+1G>A
r.spl
p.?
splicing affected?
-
Maternal (inferred)
-
pathogenic
g.94030933G>A
-
-
-
COL1A2_000228
-
PubMed: Watson et al., 1992
-
rs67398234
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Watson et al., 1992
Skips exon 6. The clinical details of the proband and members of her family were previously described by {PMID3621666:Viljoen et al., 1987}.
-
-
-
-
-
-
-
-
1
Peter Byers
+/+
6i
c.279+1G>A
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030933G>A
-
-
-
COL1A2_000228
-
PubMed: Lehmann et al., 1994
-
rs67398234
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Lehmann et al., 1994
Skips exon 6.
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/+
6i
c.279+1G>A
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030933G>A
-
-
-
COL1A2_000228
-
PubMed: Giunta et al., 1999
-
rs67398234
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Giunta et al., 1999
Skips exon 6.
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/+
6i
c.279+1G>C
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030933G>C
-
-
-
COL1A2_000462
-
PubMed: Klaassens et al., 2011
-
-
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Klaassens et al., 2011
-
-
-
-
white
-
-
-
-
1
Raymond Dalgleish
+/+
6i
c.279+1G>T
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030933G>T
-
-
-
COL1A2_000229
-
PubMed: Byers et al., 1997
-
rs67398235
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Byers et al., 1997
Skips exon 6.
-
-
-
-
-
-
-
-
1
Peter Byers
+/+
6i
c.279+1G>T
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030933G>T
-
-
-
COL1A2_000229
-
PubMed: Byers et al., 1997
-
rs67398235
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Byers et al., 1997
Skips exon 6.
-
-
-
-
-
-
-
-
1
Peter Byers
+/+
6i
c.279+1G>T
r.spl
p.?
splicing affected?
-
Maternal (confirmed)
-
pathogenic
g.94030933G>T
-
-
-
COL1A2_000229
-
PubMed: Nicholls et al., 2000
-
rs67398235
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Nicholls et al., 2000
Skips exon 6. The proband's mother is somatically mosaic for the same mutation.
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/+
6i
c.279+1G>T
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030933G>T
-
-
-
COL1A2_000229
-
PubMed: Klaassens et al., 2011
-
rs67398235
Unknown
-
-
-
-
-
DNA
PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Klaassens et al., 2011
The patient's father has mild symptoms of EDS but somatic mosaicism was not demonstrated by mutation analysis of blood, fibroblast and saliva DNA.
-
-
-
white
-
-
-
-
1
Raymond Dalgleish
+/+
6i
c.279+1G>T
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030933G>T
-
-
-
COL1A2_000229
-
PubMed: Hatamochi et al., 2014
-
rs67398235
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Hatamochi et al., 2014
Analysis of mRNA demonstrates skipping of exon 6.
-
-
-
Japanese
-
-
-
-
1
Raymond Dalgleish
+?/.
6i
c.279+1_279+5del
r.spl
p.?
-
-
Unknown
-
likely pathogenic
g.94030933_94030937del
g.94401621_94401625del
-
-
COL1A2_000910
-
-
-
-
De novo
-
-
-
-
-
DNA
SEQ, SEQ-NG
blood
-
?
-
-
-
-
-
Italy
-
-
-
-
-
1
Lucia Micale
+/+
6i
c.279+2T>C
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030934T>C
-
-
-
COL1A2_000230
-
PubMed: Weil et al., 1988
-
rs72656357
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Weil et al., 1988
Skips exon 6. This patient was previously described by {PMID3680255:Wirtz et al., 1987}
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/+
6i
c.279+2T>C
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030934T>C
-
-
-
COL1A2_000230
-
PubMed: Ho et al., 1994
-
rs72656357
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Ho et al., 1994
-
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/+
6i
c.279+2T>C
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030934T>C
-
-
-
COL1A2_000230
-
PubMed: Giunta et al., 1999
-
rs72656357
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Giunta et al., 1999
-
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/+
6i
c.279+2T>C
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030934T>C
-
-
-
COL1A2_000230
-
PubMed: Melis et al., 2012
-
rs72656357
Unknown
-
-
-
-
-
DNA
SEQ
-
-
EDS, EDSARTH2
-
PubMed: Melis et al., 2012
-
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/+
6i
c.279+2T>G
r.spl
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94030934T>G
-
-
-
COL1A2_000460
-
PubMed: Klaassens et al., 2011
-
-
Unknown
-
-
-
-
-
DNA
PCR, SEQ
-
-
EDS, EDSARTH2
-
PubMed: Klaassens et al., 2011
The mother may have some connective tissue disorder, but the patient's mutation is not found in lymphocyte DNA. The mother has a Beighton hypermobility score of 4/9.
-
-
-
white
-
-
-
-
1
Raymond Dalgleish
+/.
6i
c.279+2T>G
r.spl
p.?
-
-
Unknown
-
pathogenic
g.94030934T>G
g.94401622T>G
-
-
COL1A2_000460
-
-
-
-
De novo
-
-
-
-
-
DNA
SEQ, SEQ-NG
blood
-
EDS
-
-
-
-
-
Italy
-
-
-
-
-
1
Lucia Micale
+/+
6i_11i
c.280-1149_540+63del
r.?
p.(Gly94_Arg180del)
deletion, multi exon
-
Paternal (confirmed)
-
pathogenic
g.94032719_94035101del
-
-
-
COL1A2_000208
-
PubMed: Mundlos et al., 1996
-
rs74315105
Unknown
-
-
-
-
-
DNA, RNA
PCR, RT-PCR, SEQ, Southern
-
-
OI, OI1
-
PubMed: Mundlos et al., 1996
This mutation deletes exons 7 to 11 and in terms of genomic coordinates is g.13847_16229del
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
?/-
7
c.287T>A
r.(?)
p.(Met96Lys)
missense
-
Unknown
-
VUS
g.94033875T>A
-
-
-
COL1A2_000583
-
-
-
-
Unknown
-
-
-
-
-
DNA
SEQ-NG
-
-
EDS
-
-
The technique used was the custom NGS Gene panel.
-
-
-
white
-
-
-
-
1
Simon Bodek
+/+
7
c.293dup
r.(?)
p.(Arg99*)
frameshift
-
Unknown
-
pathogenic
g.94033881dup
-
-
-
COL1A2_000209
-
PubMed: Malfait et al., 2006
-
-
Unknown
-
-
-
-
-
DNA
PCR, SEQ, SSCA
-
-
EDS
-
PubMed: Malfait et al., 2006
The patient is descibed as having a rare form of Ehlers-Danlos syndrome with hypermobility and a propensity to cardiac valvular problems.
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+/.
7
c.299G>A
r.(?)
p.(Gly100Asp)
missense
-
Maternal (confirmed)
ACMG
pathogenic (dominant)
g.94033887G>A
g.94404575G>A
-
-
COL1A2_000936
patient has affected mother carrying the same variant
-
-
-
Germline
yes
-
-
-
-
DNA
SEQ, SEQ-NG-IT
-
marco.ritelli
EDS
ED2176
-
2-generation family, boy and affected mother carrying the same variant
M
no
Italy
-
-
-
-
-
2
Marco Ritelli
-?/.
7
c.304C>T
r.(?)
p.(Pro102Ser)
-
-
Unknown
-
likely benign
g.94033892C>T
g.94404580C>T
COL1A2(NM_000089.3):c.304C>T (p.P102S), COL1A2(NM_000089.4):c.304C>T (p.P102S)
-
COL1A2_000559
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
?/-?
7
c.304C>T
r.(?)
p.(Pro102Ser)
missense
Pro12Ser
Paternal (inferred)
-
VUS
g.94033892C>T
-
-
-
COL1A2_000559
-
PubMed: Lindahl et al., 2015
-
-
Unknown
-
-
-
-
-
DNA
PCR, SEQ
-
-
OI, OI1
-
PubMed: Lindahl et al., 2015
The patient harbours the c.577G>A and c.304C>T variants in cis.
-
-
-
Swedish
-
-
-
-
1
Katarina Lindahl
-/-?
7
c.304C>T
r.(?)
p.(Pro102Ser)
missense
Pro12Ser
Unknown
-
likely benign
g.94033892C>T
-
-
-
COL1A2_000559
-
PubMed: Lindahl et al., 2015
-
-
Unknown
-
-
-
-
-
DNA
PCR, SEQ
-
-
OI, OI1
-
PubMed: Lindahl et al., 2015
-
-
-
-
Swedish
-
-
-
-
1
Katarina Lindahl
-?/.
7
c.304C>T
r.(?)
p.(Pro102Ser)
-
-
Unknown
-
likely benign
g.94033892C>T
-
COL1A2(NM_000089.3):c.304C>T (p.P102S), COL1A2(NM_000089.4):c.304C>T (p.P102S)
-
COL1A2_000559
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/+
7
c.316G>A
r.(?)
p.(Gly106Arg)
missense
-
Maternal (confirmed)
-
pathogenic
g.94033904G>A
-
-
-
COL1A2_000680
-
Morlino et al., submitted 2019
-
-
Unknown
-
-
-
-
-
DNA
PCR, SEQ
-
-
EDS
-
Morlino et al., submitted 2019
Son of affected individual AN_005714.
-
-
-
Italian
-
-
-
-
1
Marina Colombi, Marco Ritelli
+/+
7i
c.324+4del
r.spl?
p.?
splicing affected?
-
Unknown
-
pathogenic
g.94033916del
-
-
-
COL1A2_000479
-
PubMed: Malfait et al., 2013
-
-
Unknown
-
-
-
-
-
DNA
PCR, SEQ
-
-
EDS
-
PubMed: Malfait et al., 2013
-
-
-
-
-
-
-
-
-
1
Sofie Symoens
+/+
8
c.326G>A
r.(?)
p.(Gly109Asp)
missense
Gly19Asp
Unknown
-
pathogenic
g.94034006G>A
-
-
-
COL1A2_000463
-
PubMed: Malfait et al., 2013
-
-
Unknown
-
-
-
-
-
DNA
PCR, SEQ
-
-
EDS
-
PubMed: Malfait et al., 2013
-
-
-
-
-
-
-
-
-
1
Sofie Symoens
+/+
8
c.326G>A
r.(?)
p.(Gly109Asp)
missense
Gly19Asp
Maternal (inferred)
-
pathogenic
g.94034006G>A
-
-
-
COL1A2_000463
-
PubMed: Lindahl et al., 2015
-
-
Unknown
-
-
-
-
-
DNA
PCR, SEQ
-
-
EDS
-
PubMed: Lindahl et al., 2015
-
-
-
-
Swedish
-
-
-
-
1
Katarina Lindahl
+/.
-
c.326G>A
r.(?)
p.(Gly109Asp)
-
-
Unknown
-
pathogenic
g.94034006G>A
-
COL1A2(NM_000089.4):c.326G>A (p.G109D)
-
COL1A2_000463
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+?/+
8
c.326G>T
r.(?)
p.(Gly109Val)
missense
-
Paternal (confirmed)
-
VUS
g.94034006G>T
-
-
-
COL1A2_000682
-
-
-
-
Unknown
-
-
-
-
-
DNA
SEQ-NG
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
?/.
8
c.329C>T
r.(?)
p.(Pro110Leu)
-
-
Unknown
-
VUS
g.94034009C>T
g.94404697C>T
-
-
COL1A2_000911
-
-
-
-
Germline/De novo (untested)
-
-
-
-
-
DNA
SEQ, SEQ-NG
blood
-
?
-
-
-
-
-
Italy
-
-
-
-
-
1
Lucia Micale
+/+
8
c.335G>A
r.(?)
p.(Gly112Asp)
missense
Gly22Asp
Unknown
-
pathogenic
g.94034015G>A
-
-
-
COL1A2_000590
-
PubMed: Lin et al., 2015
-
-
Unknown
-
-
-
-
-
DNA
PCR, SEQ
-
-
OI, OI1
-
PubMed: Lin et al., 2015
-
-
-
-
Taiwanese
-
-
-
-
1
Raymond Dalgleish
+?/.
8
c.335G>T
r.(?)
p.(Gly112Val)
-
-
Unknown
-
likely pathogenic
g.94034015G>T
g.94404703G>T
-
-
COL1A2_000432
-
-
-
-
Unknown
-
-
-
-
-
DNA
SEQ
blood
-
EDS
Family3-P7
-
-
F
?
Switzerland
-
19y
-
-
-
1
Lucia Micale
+/+
8
c.335G>T
r.(?)
p.(Gly112Val)
missense
Gly22Val
Unknown
-
pathogenic
g.94034015G>T
-
-
-
COL1A2_000432
-
-
-
-
Unknown
-
-
-
-
-
DNA
DHPLC, SEQ
-
-
OI, OI1
-
-
-
-
-
-
-
-
-
-
-
1
Margherita Maioli
+/+
8
c.335G>T
r.(?)
p.(Gly112Val)
missense
Gly22Val
Maternal (confirmed)
-
pathogenic
g.94034015G>T
-
-
-
COL1A2_000432
-
-
-
-
Unknown
-
-
-
-
-
DNA
SEQ
-
-
OI, OI1
-
-
-
-
-
-
-
-
-
-
-
1
Margherita Maioli
+/+
8
c.335G>T
r.(?)
p.(Gly112Val)
missense
Gly22Val
Maternal (confirmed)
-
pathogenic
g.94034015G>T
-
-
-
COL1A2_000432
-
-
-
-
Unknown
-
-
-
-
-
DNA
SEQ
-
-
OI, OI1
-
-
-
-
-
-
-
-
-
-
-
1
Margherita Maioli
+/+
8
c.335G>T
r.(?)
p.(Gly112Val)
missense
Gly22Val
Unknown
-
pathogenic
g.94034015G>T
-
-
-
COL1A2_000432
-
-
-
-
Unknown
-
-
-
-
-
DNA
SEQ
-
-
OI, OI1
-
-
-
-
-
-
-
-
-
-
-
1
Margherita Maioli
+/+
8
c.343G>A
r.(?)
p.(Gly115Arg)
missense
Gly25Arg
Unknown
-
pathogenic
g.94034023G>A
-
-
-
COL1A2_000396
-
-
-
-
Unknown
-
-
-
-
-
DNA
SEQ
-
-
OI, OI1
-
-
-
-
-
-
-
-
-
-
-
1
Isabel Mandy Nesbitt
+/+
8
c.353G>A
r.(?)
p.(Gly118Asp)
missense
Gly28Asp
Unknown
-
pathogenic
g.94034033G>A
-
-
-
COL1A2_000001
-
PubMed: Marini et al., 2007
(Körkkö and Prockop, personal communication)
-
rs72656358
Unknown
-
-
-
-
-
?
?
-
-
OI, OI1
-
PubMed: Marini et al., 2007
(Körkkö and Prockop, personal communication)
-
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
+?/.
8
c.353G>A
r.(?)
p.(Gly118Asp)
-
-
Unknown
-
likely pathogenic
g.94034033G>A
g.94404721G>A
-
-
COL1A2_000001
-
Leone 2023, submitted
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
blood
-
OI
P-0149
Leone 2023, submitted
-
-
-
Italy
-
-
-
-
-
1
Maria Pia Leone
+/+
8
c.353G>T
r.(?)
p.(Gly118Val)
missense
-
Unknown
-
pathogenic
g.94034033G>T
-
-
-
COL1A2_000594
-
PubMed: Mansfield and Rahme, 2015
-
-
Unknown
-
-
-
-
-
DNA
SEQ
-
-
OI, OI1
-
PubMed: Mansfield and Rahme, 2015
The patient had an aneurysm of the recurrent artery of Heubner. Her brother and daughter also harbour the same variant, details of which are not presented in the paper but were provided by the authors.
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
-?/.
-
c.360T>C
r.(?)
p.(=)
-
-
Unknown
-
likely benign
g.94034040T>C
-
COL1A2(NM_000089.4):c.360T>C (p.P120=)
-
COL1A2_000975
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/+
8
c.362G>A
r.(?)
p.(Gly121Asp)
missense
Gly31Asp
Unknown
-
pathogenic
g.94034042G>A
-
-
-
COL1A2_000324
-
-
-
-
Unknown
-
-
-
-
-
DNA
SEQ
-
-
OI, OI1
-
-
-
-
-
-
white
-
-
-
-
1
Peter Roughley
+/+
8
c.371G>A
r.(?)
p.(Gly124Asp)
missense
Gly34Asp
Unknown
-
pathogenic
g.94034051G>A
-
-
-
COL1A2_000002
-
PubMed: Marini et al., 2007
(Byers, personal communication)
-
rs72656359
Unknown
-
-
-
-
-
?
?
-
-
OI, OI4
-
PubMed: Marini et al., 2007
(Byers, personal communication)
-
-
-
-
-
-
-
-
-
1
Peter Byers
+/+
8
c.371G>A
r.(?)
p.(Gly124Asp)
missense
Gly34Asp
Unknown
-
pathogenic
g.94034051G>A
-
-
-
COL1A2_000002
-
PubMed: Balasubramanian et al., 2015
-
rs72656359
Unknown
-
-
-
-
-
DNA
arrayCGH, SEQ-NG
-
-
OI
-
PubMed: Balasubramanian et al., 2015
ArrayCGH identified an 8.8 Mb deletion of chromosome 11q24.2q25, involving nucleotide basepairs 126,026,082–134,868,420 (GRCh37 genome assembly) in addition to the COL1A2 variant.The technique used was the custom NGS Gene panel.
-
-
-
Pakistani
-
-
-
-
1
Raymond Dalgleish
+/+
8
c.371G>A
r.(?)
p.(Gly124Asp)
missense
Gly34Asp
Maternal (inferred)
-
pathogenic
g.94034051G>A
-
-
-
COL1A2_000002
-
-
-
rs72656359
Unknown
-
-
-
-
-
DNA
SEQ
-
-
OI, OI4
-
-
-
-
-
-
-
-
-
-
-
1
Ken Poole
+/+
9
c.380G>A
r.(?)
p.(Gly127Asp)
missense
Gly37Asp
Unknown
-
pathogenic
g.94034152G>A
-
-
-
COL1A2_000343
-
Li, 2009 ASHG Meeting 2009 Program Number: 2630
-
-
Unknown
-
-
-
-
-
?
?
-
-
OI
-
Li, 2009 ASHG Meeting 2009 Program Number: 2630
The proband is reported as having blue sclerae, joint laxity and dental crowding, but no history of fracture. He was also noted to osteosclerotic changes on X rays.
-
-
-
white
-
-
-
-
1
Raymond Dalgleish
+/+
9
c.380G>A
r.(?)
p.(Gly127Asp)
missense
Gly37Asp
Unknown
-
pathogenic
g.94034152G>A
-
-
-
COL1A2_000343
-
-
-
-
Unknown
-
-
-
-
-
DNA
SEQ
-
-
OI, OI1
-
-
-
-
-
-
white
-
-
-
-
1
Peter Roughley
+/+
9
c.389G>A
r.(?)
p.(Gly130Asp)
missense
Gly40Asp
Unknown
-
pathogenic
g.94034161G>A
-
-
-
COL1A2_000003
-
PubMed: Marini et al., 2007
(Hyland and Prockop, personal communication)
-
rs72656360
Unknown
-
-
-
-
-
?
?
-
-
OI, OI4
-
PubMed: Marini et al., 2007
(Hyland and Prockop, personal communication)
-
-
-
-
-
-
-
-
-
1
Raymond Dalgleish
-?/.
9
c.390T>A
r.(?)
p.(Gly130=)
-
-
Unknown
-
likely benign
g.94034162T>A
-
COL1A2(NM_000089.3):c.390T>A (p.G130=)
-
COL1A2_000884
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+/.
-
c.395G>A
r.(?)
p.(Arg132His)
missense
-
Unknown
-
pathogenic (dominant)
g.94034167G>A
-
-
-
COL1A2_000907
-
PubMed: Ohata 2019
-
-
Germline/De novo (untested)
-
-
-
-
-
DNA
SEQ-NG
-
capture panel for sequencing 15 candidate OI genes and 19 candidate genes that are associated with bone fragility or Wnt signaling
OI1
Pat11
PubMed: Ohata 2019
-
-
-
Japan
-
-
-
-
-
1
Lisanne Wisse
+/+
9
c.397G>A
r.(?)
p.(Gly133Ser)
missense
Gly43Ser
Unknown
-
pathogenic
g.94034169G>A
-
-
-
COL1A2_000004
-
PubMed: Marini et al., 2007
(Byers, personal communication)
-
rs72656361
Unknown
-
-
-
-
-
?
?
-
-
OI, OI4
-
PubMed: Marini et al., 2007
(Byers, personal communication)
-
-
-
-
-
-
-
-
-
1
Peter Byers
+?/.
9
c.406G>A
r.(?)
p.(Gly136Ser)
-
-
Maternal (inferred)
-
likely pathogenic
g.94034178G>A
g.94404866G>A
-
-
COL1A2_000912
-
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
blood
-
?
-
-
-
-
-
Italy
-
-
-
-
-
1
Lucia Micale
+?/+
9
c.407G>A
r.(?)
p.(Gly136Asp)
missense
Gly46Asp
Unknown
-
pathogenic
g.94034179G>A
-
-
-
COL1A2_000587
-
-
-
-
Unknown
-
-
-
-
-
DNA
SEQ
-
-
OI, OI1
-
-
-
-
-
-
-
-
-
-
-
1
Eva Gonzalez-Roca
+/+
9
c.416G>T
r.(?)
p.(Gly139Val)
missense
Gly49Val
Unknown
-
pathogenic
g.94034188G>T
-
-
-
COL1A2_000408
-
-
-
-
Unknown
-
-
-
-
-
DNA
SEQ
-
-
OI, OI1
-
-
-
-
-
-
-
-
-
-
-
1
Isabel Mandy Nesbitt
+?/.
9
c.425G>A
r.(?)
p.(Gly142Asp)
-
-
Paternal (inferred)
-
likely pathogenic
g.94034197G>A
g.94404885G>A
-
-
COL1A2_000913
-
-
-
-
Germline
-
-
-
-
-
DNA
SEQ, SEQ-NG
blood
-
?
-
-
-
-
-
Italy
-
-
-
-
-
1
Lucia Micale
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