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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View all variants in gene COL1A2
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View all diseases associated with gene COL1A2
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Unique variants in the COL1A2 gene
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)
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.
Reported
: The number of times this variant has been reported in the database.
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.
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%)
How to query this table
All list views have search fields which can be used to search data. You can search for a complete word or you can search for a part of a search term. If you enclose two or more words in double quotes, LOVD will search for the combination of those words only exactly in the order you specify. Note that search terms are case-insensitive and that wildcards such as * are treated as normal text! For all options, like "and", "or", and "not" searches, or searching for prefixes or suffixes, see the table below.
Operator
Column type
Example
Matches
Text
Arg
all entries containing 'Arg'
space
Text
Arg Ser
all entries containing 'Arg' and 'Ser'
|
Text
Arg|Ser
all entries containing 'Arg' or 'Ser'
!
Text
!fs
all entries not containing 'fs'
^
Text
^p.(Arg
all entries beginning with 'p.(Arg'
$
Text
Ser)$
all entries ending with 'Ser)'
=""
Text
=""
all entries with this field empty
=""
Text
="p.0"
all entries exactly matching 'p.0'
!=""
Text
!=""
all entries with this field not empty
!=""
Text
!="p.0"
all entries not exactly matching 'p.0?'
combination
Text
*|Ter !fs
all entries containing '*' or 'Ter' but not containing 'fs'
Date
2020
all entries matching the year 2020
|
Date
2020-03|2020-04
all entries matching March or April, 2020
!
Date
!2020-03
all entries not matching March, 2020
<
Date
<2020
all entries before the year 2020
<=
Date
<=2020-06
all entries in or before June, 2020
>
Date
>2020-06
all entries after June, 2020
>=
Date
>=2020-06-15
all entries on or after June 15th, 2020
combination
Date
2019|2020 <2020-03
all entries in 2019 or 2020, and before March, 2020
Numeric
23
all entries exactly matching 23
|
Numeric
23|24
all entries exactly matching 23 or 24
!
Numeric
!23
all entries not exactly matching 23
<
Numeric
<23
all entries lower than 23
<=
Numeric
<=23
all entries lower than, or equal to, 23
>
Numeric
>23
all entries higher than 23
>=
Numeric
>=23
all entries higher than, or equal to, 23
combination
Numeric
>=20 <30 !23
all entries with values from 20 to 29, but not equal to 23
Some more advanced examples:
Example
Matches
Asian
all entries containing 'Asian', 'asian', including 'Caucasian', 'caucasian', etc.
Asian !Caucasian
all entries containing 'Asian' but not containing 'Caucasian'
Asian|African !Caucasian
all entries containing 'Asian' or 'African', but not containing 'Caucasian'
"South Asian"
all entries containing 'South Asian', but not containing 'South East Asian'
To sort on a certain column, click on the column header or on the arrows. If that column is already selected to sort on, the sort order will be swapped. The column currently sorted on has a darker blue background color than the other columns. The up and down arrows next to the column name indicate the current sorting direction. When sorting on any field other than the default, LOVD will sort secondarily on the default sort column.
854 entries on 9 pages. Showing entries 1 - 100.
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Effect
Reported
Exon
DNA change (cDNA)
RNA change
Protein
Predicted
Legacy protein change
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
Owner
+/.
1
17
[NM_181678.2:c.-48-58227]::c.869del
r.?
p.?
-
-
-
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)
-
-
-
-
-
Johan den Dunnen
+/+
1
_1_18i
c.-471_(936+1_937-1){0}
r.0?
p.0?
deletion, multi exon
-
-
pathogenic
g.(?_94023873)_(94038921_94039034)del
g.(?_94394561)_(94409609_94409722)del
-
-
COL1A2_000413
-
-
-
-
Unknown
-
-
-
-
-
Isabel Mandy Nesbitt
+/+
1
1i
c.70+717A>G
r.(?)
p.?
other/complex
-
-
pathogenic
g.94025130A>G
-
-
-
COL1A2_000261
-
PubMed: Schwarze et al., 2004
-
rs72656354
Unknown
-
-
-
-
-
Peter Byers
-?/.
1
1i
c.71-17C>T
r.(=)
p.(=)
-
-
-
likely benign
g.94027043C>T
g.94397731C>T
-
-
COL1A2_000698
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
-/.
1
1i
c.71-8_71-7dup
r.(=)
p.(=)
-
-
-
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
-
-
-
-
-
VKGL-NL_VUmc
-/.
1
1i
c.71-7dup
r.(=)
p.(=)
-
-
-
benign
g.94027053dup
g.94397741dup
COL1A2(NM_000089.4):c.71-7dupT
-
COL1A2_000816
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
-?/.
1
2i
c.81+10A>G
r.(=)
p.(=)
-
-
-
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
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
2i
c.81+11del
r.(=)
p.(=)
-
-
-
likely benign
g.94027081del
g.94397769del
COL1A2(NM_000089.4):c.81+11delC
-
COL1A2_000818
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
-?/.
2
2i
c.81+15T>C
r.(=)
p.(=)
-
-
-
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
-
-
-
-
-
VKGL-NL_Utrecht
,
VKGL-NL_VUmc
-/.
1
2i
c.82-12A>G
r.(=)
p.(=)
-
-
-
benign
g.94027682A>G
g.94398370A>G
COL1A2(NM_000089.4):c.82-12A>G
-
COL1A2_000820
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
-/-, -/.
2
3
c.87T>C
r.(?)
p.(=), p.(Thr29=)
silent
-
-
benign, likely benign
g.94027699T>C
g.94398387T>C
COL1A2(NM_000089.4):c.87T>C (p.T29=)
-
COL1A2_000308
VKGL data sharing initiative Nederland
1 more item
-
rs1801182
CLASSIFICATION record, Unknown
-
-
-
-
-
Raymond Dalgleish
,
VKGL-NL_VUmc
-?/-?
1
4
c.118C>A
r.(?)
p.(Pro40Thr)
missense
-
-
benign
g.94028382C>A
-
-
-
COL1A2_000391
-
-
-
-
Unknown
-
-
-
-
-
Isabel Mandy Nesbitt
-/.
1
-
c.132+31G>A
r.(=)
p.(=)
-
-
-
benign
g.94028427G>A
-
COL1A2(NM_000089.4):c.132+31G>A
-
COL1A2_000924
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
-?/.
1
4i
c.133-304G>A
r.(=)
p.(=)
-
-
-
likely benign
g.94029204G>A
-
COL1A2(NM_000089.4):c.133-304G>A
-
COL1A2_000875
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
+/+
1
5
c.133G>T
r.(?)
p.(Gly45Cys)
missense
-
-
pathogenic
g.94029508G>T
-
-
-
COL1A2_000757
-
Morlino et al., submitted 2019
-
-
Unknown
-
-
-
-
-
Marina Colombi, Marco Ritelli
+?/.
1
-
c.152_157dup
r.(?)
p.(Gly51_Arg52dup)
-
-
-
likely pathogenic
g.94029527_94029532dup
g.94400215_94400220dup
-
-
COL1A2_000909
-
-
-
-
Germline
-
-
-
-
-
Lucia Micale
-?/.
1
5
c.180C>A
r.(?)
p.(Gly60=)
-
-
-
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
-
-
-
-
-
VKGL-NL_VUmc
+?/.
3
5
c.197G>A
r.(?)
p.(Gly66Asp)
-
-
-
likely pathogenic
g.94029572G>A
g.94400260G>A
-
-
COL1A2_000822
-
PubMed: Morlino 2020
-
-
Germline, Unknown
-
-
-
-
-
Lucia Micale
+/+?
1
5
c.214G>A
r.(?)
p.(Gly72Ser)
missense
-
-
likely pathogenic
g.94029589G>A
-
-
-
COL1A2_000513
-
-
-
-
Unknown
-
-
-
-
-
Lilia D'Souza-Li
+/+
1
5i
c.226-22_226-11del
r.spl
p.?
splicing affected?
-
-
pathogenic
g.94030857_94030868del
-
-
-
COL1A2_000434
-
PubMed: Giunta and Steinmann, 2008
-
-
Unknown
-
-
-
-
-
Raymond Dalgleish
+/+
1
5i_6i
c.226-17_279+12del
r.spl
p.(Asn76_Met93del)
deletion, exon
-
-
pathogenic
g.94030862_94030944del
-
-
-
COL1A2_000207
-
PubMed: Byers et al., 1997
-
rs74315131
Unknown
-
-
-
-
-
Peter Byers
-/.
1
5i
c.226-11del
r.(=)
p.(=)
-
-
-
benign
g.94030868del
g.94401556del
COL1A2(NM_000089.4):c.226-11delT
-
COL1A2_000823
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
-/.
2
5i
c.226-11dup
r.(=)
p.(=)
-
-
-
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
-
-
-
-
-
VKGL-NL_Utrecht
,
VKGL-NL_VUmc
-?/.
1
5i
c.226-10A>T
r.(=)
p.(=)
-
-
-
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
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
5i
c.226-9C>T
r.(=)
p.(=)
-
-
-
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
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
5i
c.226-6C>T
r.(=)
p.(=)
-
-
-
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
-
-
-
-
-
VKGL-NL_Rotterdam
+/+, +/.
4
5i
c.226-2A>G
r.spl, r.spl?
p.?
splicing affected?
-
-
pathogenic
g.94030877A>G
-
COL1A2(NM_000089.4):c.226-2A>G
-
COL1A2_000224
VKGL data sharing initiative Nederland
PubMed: Byers et al., 1997
,
PubMed: Klaassens et al., 2011
,
1 more item
-
rs72656355
CLASSIFICATION record, Unknown
-
-
-
-
-
Raymond Dalgleish
,
VKGL-NL_VUmc
,
Peter Byers
+/+
1
5i
c.226-1G>A
r.spl
p.?
splicing affected?
-
-
pathogenic
g.94030878G>A
-
-
-
COL1A2_000225
-
PubMed: Byers et al., 1997
-
rs66820119
Unknown
-
-
-
-
-
Peter Byers
+/+
1
5i
c.226-1G>C
r.spl
p.?
splicing affected?
-
-
pathogenic
g.94030878G>C
-
-
-
COL1A2_000226
-
PubMed: Chiodo et al., 1992
-
rs66820119
Unknown
-
-
-
-
-
Raymond Dalgleish
-/-, -/.
2
6
c.246T>C
r.(?)
p.(=), p.(Asp82=)
silent
-
-
benign, likely benign
g.94030899T>C
g.94401587T>C
COL1A2(NM_000089.4):c.246T>C (p.D82=)
-
COL1A2_000309
VKGL data sharing initiative Nederland
1 more item
-
rs1800222
CLASSIFICATION record, Unknown
-
-
-
-
-
Raymond Dalgleish
,
VKGL-NL_VUmc
+/+
2
6
c.279G>A
r.(?)
p.(Met93Ile)
splicing affected?
Met3Ile
-
pathogenic
g.94030932G>A
-
-
-
COL1A2_000227
-
PubMed: Byers et al., 1997
,
PubMed: Weil et al., 1989b
-
rs72656356
Unknown
-
-
-
-
-
Raymond Dalgleish
,
Peter Byers
+/+
6
6i
c.279+1G>A
r.spl
p.?
splicing affected?
-
-
pathogenic
g.94030933G>A
-
-
-
COL1A2_000228
-
PubMed: Giunta et al., 1999
,
PubMed: Lehmann et al., 1994
,
PubMed: Nicholls et al., 1991
,
3 more items
-
rs67398234
Unknown
-
-
-
-
-
Raymond Dalgleish
,
Peter Byers
+/+
1
6i
c.279+1G>C
r.spl
p.?
splicing affected?
-
-
pathogenic
g.94030933G>C
-
-
-
COL1A2_000462
-
PubMed: Klaassens et al., 2011
-
-
Unknown
-
-
-
-
-
Raymond Dalgleish
+/+
5
6i
c.279+1G>T
r.spl
p.?
splicing affected?
-
-
pathogenic
g.94030933G>T
-
-
-
COL1A2_000229
-
PubMed: Byers et al., 1997
,
PubMed: Hatamochi et al., 2014
,
PubMed: Klaassens et al., 2011
,
1 more item
-
rs67398235
Unknown
-
-
-
-
-
Raymond Dalgleish
,
Peter Byers
+?/.
1
6i
c.279+1_279+5del
r.spl
p.?
-
-
-
likely pathogenic
g.94030933_94030937del
g.94401621_94401625del
-
-
COL1A2_000910
-
-
-
-
De novo
-
-
-
-
-
Lucia Micale
+/+
4
6i
c.279+2T>C
r.spl
p.?
splicing affected?
-
-
pathogenic
g.94030934T>C
-
-
-
COL1A2_000230
-
PubMed: Giunta et al., 1999
,
PubMed: Ho et al., 1994
,
PubMed: Melis et al., 2012
,
1 more item
-
rs72656357
Unknown
-
-
-
-
-
Raymond Dalgleish
+/+, +/.
2
6i
c.279+2T>G
r.spl
p.?
splicing affected?
-
-
pathogenic
g.94030934T>G
g.94401622T>G
-
-
COL1A2_000460
-
PubMed: Klaassens et al., 2011
-
-
De novo, Unknown
-
-
-
-
-
Raymond Dalgleish
,
Lucia Micale
+/+
1
6i_11i
c.280-1149_540+63del
r.?
p.(Gly94_Arg180del)
deletion, multi exon
-
-
pathogenic
g.94032719_94035101del
-
-
-
COL1A2_000208
-
PubMed: Mundlos et al., 1996
-
rs74315105
Unknown
-
-
-
-
-
Raymond Dalgleish
?/-
1
7
c.287T>A
r.(?)
p.(Met96Lys)
missense
-
-
VUS
g.94033875T>A
-
-
-
COL1A2_000583
-
-
-
-
Unknown
-
-
-
-
-
Simon Bodek
+/+
1
7
c.293dup
r.(?)
p.(Arg99*)
frameshift
-
-
pathogenic
g.94033881dup
-
-
-
COL1A2_000209
-
PubMed: Malfait et al., 2006
-
-
Unknown
-
-
-
-
-
Raymond Dalgleish
+/.
1
7
c.299G>A
r.(?)
p.(Gly100Asp)
missense
-
ACMG
pathogenic (dominant)
g.94033887G>A
g.94404575G>A
-
-
COL1A2_000936
patient has affected mother carrying the same variant
-
-
-
Germline
yes
-
-
-
-
Marco Ritelli
-/-?, -?/., ?/-?
4
7
c.304C>T
r.(?)
p.(Pro102Ser)
missense
Pro12Ser
-
likely benign, VUS
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
PubMed: Lindahl et al., 2015
-
-
CLASSIFICATION record, Unknown
-
-
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_VUmc
,
Katarina Lindahl
+/+
1
7
c.316G>A
r.(?)
p.(Gly106Arg)
missense
-
-
pathogenic
g.94033904G>A
-
-
-
COL1A2_000680
-
Morlino et al., submitted 2019
-
-
Unknown
-
-
-
-
-
Marina Colombi, Marco Ritelli
+/+
1
7i
c.324+4del
r.spl?
p.?
splicing affected?
-
-
pathogenic
g.94033916del
-
-
-
COL1A2_000479
-
PubMed: Malfait et al., 2013
-
-
Unknown
-
-
-
-
-
Sofie Symoens
+/+
2
8
c.326G>A
r.(?)
p.(Gly109Asp)
missense
Gly19Asp
-
pathogenic
g.94034006G>A
-
-
-
COL1A2_000463
-
PubMed: Lindahl et al., 2015
,
PubMed: Malfait et al., 2013
-
-
Unknown
-
-
-
-
-
Sofie Symoens
,
Katarina Lindahl
+?/+
1
8
c.326G>T
r.(?)
p.(Gly109Val)
missense
-
-
VUS
g.94034006G>T
-
-
-
COL1A2_000682
-
-
-
-
Unknown
-
-
-
-
-
Ken Poole
?/.
1
8
c.329C>T
r.(?)
p.(Pro110Leu)
-
-
-
VUS
g.94034009C>T
g.94404697C>T
-
-
COL1A2_000911
-
-
-
-
Germline/De novo (untested)
-
-
-
-
-
Lucia Micale
+/+
1
8
c.335G>A
r.(?)
p.(Gly112Asp)
missense
Gly22Asp
-
pathogenic
g.94034015G>A
-
-
-
COL1A2_000590
-
PubMed: Lin et al., 2015
-
-
Unknown
-
-
-
-
-
Raymond Dalgleish
+/+, +?/.
5
8
c.335G>T
r.(?)
p.(Gly112Val)
missense
Gly22Val
-
likely pathogenic, pathogenic
g.94034015G>T
g.94404703G>T
-
-
COL1A2_000432
-
-
-
-
Unknown
-
-
-
-
-
Lucia Micale
,
Margherita Maioli
+/+
1
8
c.343G>A
r.(?)
p.(Gly115Arg)
missense
Gly25Arg
-
pathogenic
g.94034023G>A
-
-
-
COL1A2_000396
-
-
-
-
Unknown
-
-
-
-
-
Isabel Mandy Nesbitt
+/+, +?/.
2
8
c.353G>A
r.(?)
p.(Gly118Asp)
missense
Gly28Asp
-
likely pathogenic, pathogenic
g.94034033G>A
g.94404721G>A
-
-
COL1A2_000001
-
Leone 2023, submitted,
PubMed: Marini et al., 2007
(Körkkö and Prockop, personal communication)
-
rs72656358
Germline, Unknown
-
-
-
-
-
Raymond Dalgleish
,
Maria Pia Leone
+/+
1
8
c.353G>T
r.(?)
p.(Gly118Val)
missense
-
-
pathogenic
g.94034033G>T
-
-
-
COL1A2_000594
-
PubMed: Mansfield and Rahme, 2015
-
-
Unknown
-
-
-
-
-
Raymond Dalgleish
+/+
1
8
c.362G>A
r.(?)
p.(Gly121Asp)
missense
Gly31Asp
-
pathogenic
g.94034042G>A
-
-
-
COL1A2_000324
-
-
-
-
Unknown
-
-
-
-
-
Peter Roughley
+/+
3
8
c.371G>A
r.(?)
p.(Gly124Asp)
missense
Gly34Asp
-
pathogenic
g.94034051G>A
-
-
-
COL1A2_000002
-
PubMed: Balasubramanian et al., 2015
,
PubMed: Marini et al., 2007
(Byers, personal communication)
-
rs72656359
Unknown
-
-
-
-
-
Raymond Dalgleish
,
Peter Byers
,
Ken Poole
+/+
2
9
c.380G>A
r.(?)
p.(Gly127Asp)
missense
Gly37Asp
-
pathogenic
g.94034152G>A
-
-
-
COL1A2_000343
-
Li, 2009 ASHG Meeting 2009 Program Number: 2630
-
-
Unknown
-
-
-
-
-
Raymond Dalgleish
,
Peter Roughley
+/+
1
9
c.389G>A
r.(?)
p.(Gly130Asp)
missense
Gly40Asp
-
pathogenic
g.94034161G>A
-
-
-
COL1A2_000003
-
PubMed: Marini et al., 2007
(Hyland and Prockop, personal communication)
-
rs72656360
Unknown
-
-
-
-
-
Raymond Dalgleish
-?/.
1
9
c.390T>A
r.(?)
p.(Gly130=)
-
-
-
likely benign
g.94034162T>A
-
COL1A2(NM_000089.3):c.390T>A (p.G130=)
-
COL1A2_000884
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
-
c.395G>A
r.(?)
p.(Arg132His)
missense
-
-
pathogenic (dominant)
g.94034167G>A
-
-
-
COL1A2_000907
-
PubMed: Ohata 2019
-
-
Germline/De novo (untested)
-
-
-
-
-
Lisanne Wisse
+/+
1
9
c.397G>A
r.(?)
p.(Gly133Ser)
missense
Gly43Ser
-
pathogenic
g.94034169G>A
-
-
-
COL1A2_000004
-
PubMed: Marini et al., 2007
(Byers, personal communication)
-
rs72656361
Unknown
-
-
-
-
-
Peter Byers
+?/.
1
9
c.406G>A
r.(?)
p.(Gly136Ser)
-
-
-
likely pathogenic
g.94034178G>A
g.94404866G>A
-
-
COL1A2_000912
-
-
-
-
Germline
-
-
-
-
-
Lucia Micale
+?/+
1
9
c.407G>A
r.(?)
p.(Gly136Asp)
missense
Gly46Asp
-
pathogenic
g.94034179G>A
-
-
-
COL1A2_000587
-
-
-
-
Unknown
-
-
-
-
-
Eva Gonzalez-Roca
+/+
1
9
c.416G>T
r.(?)
p.(Gly139Val)
missense
Gly49Val
-
pathogenic
g.94034188G>T
-
-
-
COL1A2_000408
-
-
-
-
Unknown
-
-
-
-
-
Isabel Mandy Nesbitt
+?/.
1
9
c.425G>A
r.(?)
p.(Gly142Asp)
-
-
-
likely pathogenic
g.94034197G>A
g.94404885G>A
-
-
COL1A2_000913
-
-
-
-
Germline
-
-
-
-
-
Lucia Micale
+/+
3
9i
c.432+1G>A
r.spl
p.?
splicing affected, splicing affected?
-
-
pathogenic
g.94034205G>A
g.94404893G>A
-
-
COL1A2_000382
-
PubMed: Demir 2021
-
-
Germline/De novo (untested), Unknown
-
-
-
-
-
Johan den Dunnen
,
Margherita Maioli
+/+
1
9i
c.432+3_432+13del
r.spl?
p.?
splicing affected?
-
-
pathogenic
g.94034207_94034217del
-
-
-
COL1A2_000231
-
PubMed: Nicholls et al., 1992
-
rs72656362
Unknown
-
-
-
-
-
Raymond Dalgleish
+/+, +/.
3
9i
c.432+4_432+7del
r.spl?
p.?
splicing affected?
-
-
likely pathogenic, pathogenic
g.94034208_94034211del
g.94404896_94404899del
432+4_432+7delAGTA
-
COL1A2_000232
-
PubMed: Malfait et al., 2013
,
PubMed: Marini et al., 2007
(Byers, personal communication)
-
rs72656363
Unknown
-
-
-
-
-
Sofie Symoens
,
Lucia Micale
,
Peter Byers
+/+, +/.
3
9i
c.432+5G>A
r.spl?
p.?
splicing affected?
-
-
likely pathogenic, pathogenic
g.94034209G>A
g.94404897G>A
-
-
COL1A2_000233
-
PubMed: Feshchenko et al., 1998
,
PubMed: Marini et al., 2007
(Byers, personal communication)
-
rs72656364
Unknown
-
-
-
-
-
Raymond Dalgleish
,
Lucia Micale
,
Peter Byers
-?/.
1
9i
c.432+20C>T
r.(=)
p.(=)
-
-
-
likely benign
g.94034224C>T
g.94404912C>T
COL1A2(NM_000089.4):c.432+20C>T
-
COL1A2_000828
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
+/+
1
9i_17i
c.432+59_891+7del
r.spl
p.(Gly145_Pro297del)
deletion, multi exon
-
-
pathogenic
g.94034263_94038739del
-
-
-
COL1A2_000210
-
PubMed: Mundlos et al., 1996
-
rs74315153
Unknown
-
-
-
-
-
Raymond Dalgleish
+/+
1
9i
c.433-2A>G
r.spl
p.?
splicing affected?
-
-
pathogenic
g.94034509A>G
-
-
-
COL1A2_000480
-
-
-
-
Unknown
-
-
-
-
-
Sofie Symoens
+/+
2
9i
c.433-1G>C
r.spl
p.?
splicing affected?
-
-
pathogenic
g.94034510G>C
-
-
-
COL1A2_000234
-
PubMed: Balasubramanian et al., 2015
,
1 more item
-
rs72656365
Unknown
-
-
-
-
-
Raymond Dalgleish
+/.
1
-
c.434G>T
r.(?)
p.(Gly145Val)
-
-
-
pathogenic
g.94034512G>T
-
COL1A2(NM_000089.4):c.434G>T (p.G145V)
-
COL1A2_000925
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
+?/.
1
10
c.469G>A
r.(?)
p.(Gly157Arg)
-
-
-
likely pathogenic
g.94034547G>A
g.94405235G>A
-
-
COL1A2_000914
-
-
-
-
De novo
-
-
-
-
-
Lucia Micale
+/., +/?
2
10
c.478G>A
r.(?)
p.(Gly160Arg)
missense
Gly70Arg
-
pathogenic (dominant), VUS
g.94034556G>A
g.94405244G>A
-
-
COL1A2_000650
-
PubMed: Li 2019
,
Journal: Li 2019
,
PubMed: Liu 2017
-
-
Germline, Unknown
-
1/101 cases OI
-
-
-
Johan den Dunnen
,
Xiuli Zhao
+/+
1
10
c.479G>A
r.(?)
p.(Gly160Glu)
-
-
-
pathogenic
g.94034557G>A
g.94405245G>A
-
-
COL1A2_000829
-
-
-
-
Germline/De novo (untested)
-
-
-
-
-
Gemeinschaftspraxis für Humangenetik Dresden
+/+
1
10i
c.486+1G>C
r.spl
p.?
splicing affected?
-
-
pathogenic
g.94034565G>C
-
-
-
COL1A2_000481
-
-
-
-
Unknown
-
-
-
-
-
Sofie Symoens
+?/+
1
10i
c.486+2T>G
r.spl
p.?
splicing affected?
-
-
pathogenic
g.94034566T>G
-
-
-
COL1A2_000602
-
PubMed: Bardai et al.,2016
-
-
Unknown
-
-
-
-
-
Ghalib Bardai, Patrizia Mason
+/+
1
10i_11
c.487-5_500del
r.spl
p.?
splicing affected?
-
-
pathogenic
g.94034980_94034998del
-
-
-
COL1A2_000239
-
PubMed: Kuivaniemi et al., 1988
-
rs74315146
Unknown
-
-
-
-
-
Raymond Dalgleish
+/+
3
11
c.497G>T
r.(?)
p.(Gly166Val)
missense
Gly76Val
-
pathogenic
g.94034995G>T
-
-
-
COL1A2_000005
-
PubMed: Marini et al., 2007
(Byers, personal communication),
1 more item
-
rs72656366
Unknown
-
-
-
-
-
Raymond Dalgleish
,
Javier Garcia-Planells
,
Peter Byers
?/.
1
11
c.502C>T
r.(?)
p.(Pro168Ser)
-
-
-
VUS
g.94035000C>T
-
-
-
COL1A2_000876
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
+/+
1
11
c.506G>A
r.(?)
p.(Gly169Glu)
missense
Gly79Glu
-
pathogenic
g.94035004G>A
-
-
-
COL1A2_000341
-
-
-
-
Unknown
-
-
-
-
-
Margherita Maioli
?/.
1
11
c.539G>A
r.(?)
p.(Arg180Lys)
-
-
-
VUS
g.94035037G>A
g.94405725G>A
-
-
COL1A2_000915
-
-
-
-
Germline/De novo (untested)
-
-
-
-
-
Lucia Micale
+/+
1
11i
c.540+5G>A
r.spl?
p.?
splicing affected?
-
-
pathogenic
g.94035043G>A
-
-
-
COL1A2_000259
-
PubMed: Schwarze et al., 2004
-
rs72656367
Unknown
-
-
-
-
-
Peter Byers
+/+
1
11i_32i
c.540+37_1972-220dup
r.?
p.(Gly181_Lys657dup)
insertion
-
-
pathogenic
g.94035075_94047591dup
-
[1972-222G>C;1972-220T>A;540+37_1972-220dup]
-
COL1A2_000211
-
PubMed: Raff et al., 2000
-
-
Germline
-
-
-
-
-
Peter Byers
+/?
1
11i
c.541-2del
r.spl
p.?
splicing affected?
-
-
VUS
g.94035560del
-
-
-
COL1A2_000660
-
PubMed: Li 2019
,
Journal: Li 2019
-
-
Unknown
-
-
-
-
-
Xiuli Zhao
+/+
1
12
c.544C>G
r.(?)
p.(His182Asp)
missense
His92Asp
-
pathogenic
g.94035565C>G
-
-
-
COL1A2_000137
-
PubMed: Galicka et al., 2003
-
rs72656368
Unknown
-
-
-
-
-
Raymond Dalgleish
+?/.
1
12
c.556G>T
r.(?)
p.(Asp186Tyr)
-
-
-
likely pathogenic
g.94035577G>T
g.94406265G>T
NM_000089.3(COL1A2):c.556G>T p.(Asp186Tyr)
-
COL1A2_000830
variant could not be associated with disease phenotype
PubMed: Vogelaar 2017
,
Journal: Vogelaar 2017
-
-
Germline
-
-
-
-
-
Marjolijn JL Ligtenberg
+/+, +/?
3
12
c.560G>A
r.(?)
p.(Gly187Glu)
missense
Gly97Glu
-
pathogenic, VUS
g.94035581G>A
-
-
-
COL1A2_000493
-
PubMed: Li 2019
,
Journal: Li 2019
-
-
Unknown
-
-
-
-
-
Yanqin Lu
,
Margherita Maioli
,
Xiuli Zhao
+/?
1
12
c.560G>T
r.(?)
p.(Gly187Val)
missense
Gly97Val
-
VUS
g.94035581G>T
-
-
-
COL1A2_000658
-
PubMed: Li 2019
,
Journal: Li 2019
-
-
Unknown
-
-
-
-
-
Xiuli Zhao
+/.
1
12
c.568G>A
r.(?)
p.(Gly190Arg)
-
-
-
pathogenic
g.94035589G>A
g.94406277G>A
COL1A2(NM_000089.4):c.568G>A (p.G190R)
-
COL1A2_000831
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
+/., +/?
2
12
c.568G>C
r.(?)
p.(Gly190Arg)
missense
Gly100Arg
-
pathogenic (dominant), VUS
g.94035589G>C
g.94406277G>C
-
-
COL1A2_000646
-
PubMed: Li 2019
,
Journal: Li 2019
,
PubMed: Liu 2017
-
-
Germline, Unknown
-
1/101 cases OI
-
-
-
Johan den Dunnen
,
Xiuli Zhao
+/+, +/?
2
12
c.569G>A
r.(?)
p.(Gly190Glu)
missense
Gly100Glu
-
pathogenic, VUS
g.94035590G>A
-
-
-
COL1A2_000421
-
PubMed: Li 2019
,
Journal: Li 2019
-
-
Unknown
-
-
-
-
-
Javier Garcia-Planells
,
Xiuli Zhao
+/+
1
12
c.569G>C
r.(?)
p.(Gly190Ala)
missense
Gly100Ala
-
pathogenic
g.94035590G>C
-
-
-
COL1A2_000617
-
-
-
-
Unknown
-
-
-
-
-
Margherita Maioli
+/+
2
12
c.569G>T
r.(?)
p.(Gly190Val)
missense
Gly100Val
-
pathogenic
g.94035590G>T
-
-
-
COL1A2_000006
-
PubMed: Marini et al., 2007
(De Paepe, personal communication)
-
rs72656369
Unknown
-
-
-
-
-
Raymond Dalgleish
,
Sofie Symoens
+/+, +/., +?/.
20
12
c.577G>A
r.(?)
p.(Gly193Ser)
missense
Gly103Ser
-
likely pathogenic, pathogenic
g.94035598G>A
g.94406286G>A
-
-
COL1A2_000007
-
PubMed: Gentile et al., 2013
,
PubMed: Lindahl et al., 2015
,
PubMed: Morlino 2020
,
3 more items
-
rs72656370
Germline, Unknown
-
-
-
-
-
Raymond Dalgleish
,
Lucia Micale
,
Isabel Mandy Nesbitt
,
Maria Luisa Bianchi
,
Margherita Maioli
,
Katarina Lindahl
+/+, +?/.
2
12
c.577G>C
r.(?)
p.(Gly193Arg)
missense
Gly103Arg
ACMG
likely pathogenic (dominant), pathogenic
g.94035598G>C
g.94406286G>C
-
-
COL1A2_000322
-
Mazzeu 2022, unpublished
-
-
Germline, Unknown
-
-
-
-
-
Juliana Mazzeu
,
Margherita Maioli
+/+, +/., +/?, +?/+
5
12
c.578G>A
r.(?)
p.(Gly193Asp)
missense
Gly103Asp
-
likely pathogenic, pathogenic, VUS
g.94035599G>A
g.94406287G>A
COL1A2(NM_000089.4):c.578G>A (p.G193D)
-
COL1A2_000008
VKGL data sharing initiative Nederland
PubMed: Demir 2021
,
PubMed: Li 2019
,
Journal: Li 2019
,
1 more item
-
rs72656371
CLASSIFICATION record, Germline/De novo (untested), Unknown
-
-
-
-
-
Johan den Dunnen
,
Raymond Dalgleish
,
VKGL-NL_VUmc
,
Lucia Micale
,
Xiuli Zhao
+/+
2
12
c.578G>T
r.(?)
p.(Gly193Val)
missense
Gly103Val
-
pathogenic
g.94035599G>T
-
-
-
COL1A2_000550
-
PubMed: Li 2019
,
Journal: Li 2019
-
-
Unknown
-
-
-
-
-
Xue Bai
,
Xiuli Zhao
?/-
1
12
c.582T>G
r.(?)
p.(=)
silent
-
-
VUS
g.94035603T>G
-
-
-
COL1A2_000557
-
-
-
-
Unknown
-
-
-
-
-
Xue Bai
+/+
1
12
c.586G>T
r.(?)
p.(Gly196Cys)
missense
Gly109Cys
-
pathogenic
g.94035607G>T
-
-
-
COL1A2_000457
-
PubMed: Zhang et al., 2011
-
-
Unknown
-
-
-
-
-
Raymond Dalgleish
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