Global Variome shared LOVD
LDLR (low density lipoprotein receptor)
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Curator:
Sarah Leigh
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Unique variants in the LDLR gene
The variants shown are described using the NM_000527.4 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
Predict/MutationTaster
: Mutation Taster prediction variant; disease causing, polymorphism
P-domain
: region/domain protein affected
Predict/PolyPhen
: PolyPhen predicted effect of variant; benign, possibly damaging, probably damaging, unknown (no prediction)
Predict/SIFT
: SIFT predicted effect of variant
Conservation
: conservation, conservation score, (species)
Predict/Splice
: splice prediction
Enzyme activity
: activity variant enzym
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
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Operator
Column type
Example
Matches
Text
Arg
all entries containing 'Arg'
space
Text
Arg Ser
all entries containing 'Arg' and 'Ser'
|
Text
Arg|Ser
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!
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'
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2153 entries on 22 pages. Showing entries 1 - 100.
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Effect
Reported
Exon
DNA change (cDNA)
RNA change
Protein
Predict/MutationTaster
P-domain
Predict/PolyPhen
Predict/SIFT
Conservation
Predict/Splice
Enzyme activity
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
4
c.[649_654dup;657_661del]
r.(?)
p.([Asp217_Gly218dup; Gly219fs*7])
-
LDL-receptor class A5
-
-
-
-
-
ACGS
pathogenic
g.[11216231_11216236dup;11216239_11216243del]
-
[D196_G197dup;G198fsX7]
-
LDLR_000370
predicted trucated protein; 6bp duplication (GATGGT) & 5bp deletion (CCCCG)
PubMed: Giesel 1995
-
-
Germline
-
-
-
-
-
Sarah Leigh
+/+
1
_1_2i
c.-1823_190+566del
r.(?)
p.0?
-
Promoter - exon 2
-
-
-
-
-
ACGS
pathogenic
g.11198402_11211587del
g.11087726_11100911del
-
-
LDLR_000005
predicted no protein; Deletion of exons 1 & 2; May be the same as c.1-?_190+?del
PubMed: Goldmann 2010
-
-
Germline
-
1/37 patients with LDLR mutation. 1/1945 FH patients. Variant not present in controls
-
-
-
Sarah Leigh
+/.
1
_1_1i
c.-1818_67+1091delinsTTC
r.0?
p.0?
-
-
-
-
-
-
-
-
pathogenic (dominant)
g.11198407_11201382delinsTTC
g.11087731_11090706delinsTTC
11198406_11201384del, insTTCG
-
LDLR_002172
2977 del exon 1
PubMed: Wong 2019
,
Journal: Wong 2019
-
-
Germline
yes
-
-
-
-
Karen HY Wong
?/.
1
-
c.-283G>C
r.(?)
p.(=)
-
-
-
-
-
-
-
-
VUS
g.11199942G>C
-
LDLR(NM_000527.4):c.-283G>C
-
LDLR_002298
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-?/-?, -?/.
3
_1
c.-268G>T
r.(=), r.(?)
p.(=), p.?
-
FP2 cis acting regulatory element
-
-
7/8 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795}
-
limited effect on LDLR activity, Transient transfection in HepG2 cells demonstrated
ACGS
likely benign
g.11199957G>T
g.11089281G>T
LDLR(NM_000527.4):c.-268G>T
-
LDLR_000374
VKGL data sharing initiative Nederland,
1 more item
PubMed: Scholtz 1999
,
PubMed: Whittall 2002
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Sarah Leigh
,
VKGL-NL_AMC
?/?
1
_1
c.-221_-220insA
r.(=)
p.?
-
FP1 cis acting regulatory element
-
-
-
-
-
ACGS
VUS
g.11200005dup
g.11089329dup
-
-
LDLR_000950
-
PubMed: Bodamer 2002
-
-
Germline
-
-
-
-
-
Sarah Leigh
-?/-?, -?/., -?/?
3
_1
c.-217C>T
r.(=), r.(?)
p.(=), p.?
-
FP1 cis acting regulatory element
-
-
1 more item
-
1 more item
ACGS
likely benign
g.11200008C>T
g.11089332C>T
IVS1-217C>T, LDLR(NM_000527.4):c.-217C>T
-
LDLR_000015
VKGL data sharing initiative Nederland,
2 more items
PubMed: Scholtz 1999
,
PubMed: Snozek 2009
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Sarah Leigh
,
VKGL-NL_AMC
-?/?
1
_1
c.-215A>G
r.(=)
p.?
-
FP1 cis acting regulatory element
-
-
1 more item
-
1 more item
ACGS
likely benign
g.11200010A>G
g.11089334A>G
-
-
LDLR_000006
prediction no effect on transcription
PubMed: Usifo 2012
-
-
Germline
-
-
-
-
-
Sarah Leigh
-?/-?
1
_1
c.-208A>T
r.(=)
p.?
-
SREBP1/FP1
-
-
1 more item
-
100% of wt trascriptional activity (luciferase assay).
ACGS
likely benign
g.11200017A>T
g.11089341A>T
-
-
LDLR_001268
prediction no effect on transcription
PubMed: De Castro-Oros 2011
-
-
Germline
-
0.06 in this study
-
-
-
Sarah Leigh
?/?
1
_1
c.-206C>T
r.(=)
p.?
-
SREBP1/FP1
-
-
1 more item
-
not tested
ACGS
VUS
g.11200019C>T
g.11089343C>T
-
-
LDLR_001010
-
PubMed: Lind 2002
-
-
Germline
-
-
-
-
-
Sarah Leigh
?/?
1
_1
c.-193_-186delinsTG
r.(=)
p.?
-
SREBP1 binding site
-
-
-
-
not tested
ACGS
VUS
g.11200032_11200039delinsTG
g.11089356_11089363delinsTG
-
-
LDLR_001024
-
PubMed: Fouchier 2005
-
-
Germline
-
-
-
-
-
Sarah Leigh
?/?
1
_1
c.-188C>T
r.(=)
p.?
-
SREBP1 binding site
-
-
1 more item
-
not tested
ACGS
VUS
g.11200037C>T
g.11089361C>T
-
-
LDLR_001023
-
PubMed: Fouchier 2005
-
-
Germline
-
-
-
-
-
Sarah Leigh
+?/.
1
-
c.-187C>T
r.(?)
p.(=)
-
-
-
-
-
-
-
-
likely pathogenic
g.11200038C>T
g.11089362C>T
LDLR(NM_000527.4):c.-187C>T
-
LDLR_002180
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/+
10
_1_1i
c.(?_-187)_(67+1_68-1)del
r.(?)
p.0?
-
Promoter - exon 1, promotor & exon 1, Promotor - exon 1
-
-
-
-
<2% LDLR activity in Hmz, <2% LDLR activity when Htz with unknown FH allele
ACGS
pathogenic
g.11200038_11200292del
-
c.-187-?_67+?del, c.-187-?_67+?del, FH Denver-1, c.-187-?_67+?del, FH French Canadian-1,
1 more item
-
LDLR_000007
10 more items
PubMed: Chaves 2001
,
PubMed: Fouchier 2005
,
PubMed: Hobbs 1987
,
PubMed: Hobbs 1988
,
PubMed: Tichy 2012
,
4 more items
-
-
Germline
-
0.19 in this study, NA
-
-
-
Sarah Leigh
+?/+?
1
_1_1i
c.(?_-187)_(67+1_68-1)dup
r.(?)
p.0?
-
Promotor - exon 1
-
-
-
-
-
ACGS
likely pathogenic
g.11200038_11200292dup
-
c.-187-?_67+?dup
-
LDLR_001273
1 more item
PubMed: Sharifi 2016
-
-
Germline
-
NA
-
-
-
Sarah Leigh
+/+
4
_1_2i
c.(?_-187)_(190+1_191-1)del
r.(?)
p.0?
-
Promotor - exon 2
-
-
-
-
45% LDLR activity in Htz fibroblasts
ACGS
pathogenic
g.11200038_11211022del
-
c.-187-?_190+?del
-
LDLR_000008
4 more items
PubMed: Chaves 2001
,
PubMed: Chmara 2010
,
PubMed: Garuti 1996
,
PubMed: Koeijvoets 2005
-
-
Germline
-
4/169 patients with LDLR mutation. 4/378 FH patients. Variant not present in Normal Non FH patients
-
-
-
Sarah Leigh
+/+
3
_1_6i
c.(?_-187)_(940+1_941-1)del
r.(?)
p.0?
-
Promoter - exon 6
-
-
-
-
40-50% LDLR activity in Htz
ACGS
pathogenic
g.11200038_11218191del
-
c.-187-?_940+?del, FH Bari-3, c.-187-?_940+?del, FH Bologna-1
-
LDLR_001274
3 more items
PubMed: Bertolini 2000
,
PubMed: Lelli 1991
,
PubMed: Sun 1992
-
-
Germline
-
-
-
-
-
Sarah Leigh
+/+
1
_1_7i
c.(?_-187)_(1060+1_1061-1)del
r.(?)
p.0?
-
Promoter - exon 7
-
-
-
-
-
ACGS
pathogenic
g.11200038_11221448del
-
c.-187-?_1060+?del
-
LDLR_001271
1 more item
PubMed: Marduel 2010
-
-
Germline
-
-
-
-
-
Sarah Leigh
+/+
1
_1_8i
c.(?_-187)_(1186+1_1187-1)del
r.(?)
p.0?
-
Promoter - exon 8
-
-
-
-
-
ACGS
pathogenic
g.11200038_11222316del
-
c.-187-?_1186+?del
-
LDLR_001091
1 more item
PubMed: Fouchier 2005
-
-
Germline
-
-
-
-
-
Sarah Leigh
+/+
1
_1_12i
c.(?_-187)_(1845+1_1846-1)del
r.(?)
p.0?
-
Promoter - exon 12
-
-
-
-
-
ACGS
pathogenic
g.11200038_11227675del
-
c.-187-?_1845+?del
-
LDLR_001167
1 more item
PubMed: Shin 2015
-
-
Germline
-
-
-
-
-
Sarah Leigh
+/+
1
_1_14i
c.(?_-187)_(2140+1_2141-1)del
r.(?)
p.0?
-
Promoter - exon 14
-
-
-
-
-
ACGS
pathogenic
g.11200038_11231199del
-
c.-187-?_2140+?del
-
LDLR_000009
1 more item
PubMed: Van der Graaf 2011
-
-
Germline
-
-
-
-
-
Sarah Leigh
+/+
1
_1_15i
c.(?_-187)_(2311+1_2312-1)del
r.(?)
p.0?
-
Promoter - exon 15
-
-
-
-
-
ACGS
pathogenic
g.11200038_11234021del
-
c.-187-?_2311+?del
-
LDLR_001272
1 more item
PubMed: Bertolini 2013
-
-
Germline
-
-
-
-
-
Sarah Leigh
+/+
2
_1_18_
c.(?_-187)_(*2584_?)del
r.(?)
p.0?
-
whole gene
-
-
-
-
-
ACGS
pathogenic
g.11200038_11244576del, g.11200038_11244577del
g.11089362_11133900del, g.11089362_11133901del
c.-187-?_*2584del
-
LDLR_000010
predicted no protein; deletion of whole gene,
1 more item
PubMed: Marduel 2010
,
PubMed: Usifo 2012
-
-
Germline
-
-
-
-
-
Sarah Leigh
+?/+?
1
1
c.-185_-183del
r.(=)
p.(=)
-
SREBP1 binding site
-
-
-
-
1 more item
ACGS
likely pathogenic
g.11200040_11200042del
g.11089364_11089366del
c.-185_-183delCTT, FH Pedi-2
-
LDLR_000103
1 more item
PubMed: Peeters 1998
-
-
Germline
-
-
-
-
-
Sarah Leigh
+?/+?
1
1
c.-156C>T
r.(=)
p.(=)
-
SREBP2 binding site
-
-
1 more item
-
Not tested
ACGS
likely pathogenic
g.11200069C>T
g.11089393C>T
-
-
LDLR_001112
1 more item
PubMed: Dedoussis 2004
-
-
Germline
-
-
-
-
-
Sarah Leigh
+?/+?
1
1
c.-155_-154delinsTTCTGCAAACTCCT
r.(=)
p.(=)
-
SREBP2 binding site
-
-
-
-
11% of wt trascriptional activity (luciferase assay)
ACGS
likely pathogenic
g.11200070_11200071delinsTTCTGCAAACTCCT
g.11089394_11089395delinsTTCTGCAAACTCCT
-
-
LDLR_001267
1 more item
PubMed: De Castro-Oros 2011
-
-
Germline
-
0.06 in this study
-
-
-
Sarah Leigh
?/?
1
1
c.-153C>T
r.(=)
p.(=)
-
SREBP2 binding site
-
-
1 more item
-
Not tested
ACGS
VUS
g.11200072C>T
g.11089396C>T
-
-
LDLR_001116
1 more item
PubMed: Francova 2004
-
-
Germline
-
-
-
-
-
Sarah Leigh
+/., +?/+?
4
1
c.-152C>T
r.(=), r.(?)
p.(=)
-
SREBP2 binding site
-
-
1 more item
-
40% of wt transcription using luciferase assay
ACGS
likely pathogenic, pathogenic
g.11200073C>T
g.11089397C>T
LDLR(NM_000527.4):c.-152C>T
-
LDLR_001266
predicted reduced transcription; Hobb's numbering: -59C>T., VKGL data sharing initiative Nederland
PubMed: Brusgaard 2006
,
PubMed: Khoo 2000
,
PubMed: Scholtz 1999
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Sarah Leigh
,
VKGL-NL_AMC
+?/.
1
-
c.-150A>G
r.(?)
p.(=)
-
-
-
-
-
-
-
-
likely pathogenic
g.11200075A>G
g.11089399A>G
LDLR(NM_000527.4):c.-150A>G
-
LDLR_002040
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
?/?
1
1
c.-149C>A
r.(=)
p.(=)
-
SREBP2 binding site
-
-
-
-
not tested
ACGS
VUS
g.11200076C>A
g.11089400C>A
-
-
LDLR_001264
Hobb's numbering: -56C>A.
PubMed: Tichy 2012
-
-
Germline
-
-
-
-
-
Sarah Leigh
?/?
1
1
c.-146C>A
r.(=)
p.(=)
-
SREBP2 binding site
-
-
1 more item
-
Not tested
ACGS
VUS
g.11200079C>A
g.11089403C>A
-
-
LDLR_001263
Hobb's numbering -53C>A
PubMed: Day 1997
-
-
Germline
-
not in ExAC, June 2015
-
-
-
Sarah Leigh
?/.
1
-
c.-143A>C
r.(?)
p.(=)
-
-
-
-
-
-
-
-
VUS
g.11200082A>C
g.11089406A>C
LDLR(NM_000527.4):c.-143A>C
-
LDLR_002041
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/.
1
-
c.-142C>G
r.(?)
p.(=)
-
-
-
-
-
-
-
-
pathogenic
g.11200083C>G
g.11089407C>G
LDLR(NM_000527.4):c.-142C>G
-
LDLR_001923
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
?/?
2
1
c.-142C>T
r.(=)
p.(=)
-
SP1 binding site
-
-
1 more item
-
1 more item
ACGS
VUS
g.11200083C>T
g.11089407C>T
-
-
LDLR_000857
2 more items
PubMed: Leren 2004
,
PubMed: Mozas 2002
-
-
Germline
-
-
-
-
-
Sarah Leigh
+?/+?
2
1
c.-140C>G
r.(=)
p.(=)
-
SP1 binding site
-
-
1 more item
-
2 more items
ACGS
likely pathogenic
g.11200085C>G
g.11089409C>G
-
-
LDLR_000322
prediction reduced transcription
PubMed: Alonso 2009
,
PubMed: De Castro-Oros 2011
-
-
Germline
-
0.3 in this study
-
-
-
Sarah Leigh
+?/+?
1
1
c.-140C>T
r.(=)
p.(=)
-
SP1 binding site
-
-
1 more item
-
1 more item
ACGS
likely pathogenic
g.11200085C>T
g.11089409C>T
-
-
LDLR_000323
1 more item
PubMed: De Castro-Oros 2011
-
-
Germline
-
0.06 in this study
-
-
-
Sarah Leigh
?/?
1
1
c.-139C>A
r.(=)
p.(=)
-
SP1 binding site
-
-
1 more item
-
Not tested
ACGS
VUS
g.11200086C>A
g.11089410C>A
-
-
LDLR_001025
-
PubMed: Fouchier 2005
-
-
Germline
-
-
-
-
-
Sarah Leigh
+/., +?/+?
2
1
c.-139C>G
r.(=), r.(?)
p.(=)
-
SP1 binding site
-
-
1 more item
-
26% of wt using luciferase assay
ACGS
likely pathogenic, pathogenic
g.11200086C>G
g.11089410C>G
LDLR(NM_000527.4):c.-139C>G
-
LDLR_001190
VKGL data sharing initiative Nederland,
1 more item
PubMed: Smith 2007
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Sarah Leigh
,
VKGL-NL_AMC
+/., +?/+?
2
1
c.-138del
r.(=), r.(?)
p.(=)
-
SP1 binding site
-
-
1 more item
-
24% LDLR activity in Htz lymphocytes. Reduced level of expression
ACGS
likely pathogenic, pathogenic
g.11200087del
g.11089411del
c.-138delT, FH Pyrgos, LDLR(NM_000527.4):c.-138delT
-
LDLR_000959
predicted reduced levels of transcription; Hobbs' numbering: -45delT.,
1 more item
PubMed: Dedoussis 2003
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Sarah Leigh
,
VKGL-NL_AMC
+?/+?
1
1
c.-138T>C
r.(=)
p.(=)
-
SP1 binding site
-
-
1 more item
-
Luciferase assay 43% of normal in the presence & 25% in the absence of sterols in the medium.
ACGS
likely pathogenic
g.11200087T>C
g.11089411T>C
-
-
LDLR_000438
predicted reduced transcription; Hobbs' numbering: -45T>C
PubMed: Sun 1995
-
-
Germline
-
-
-
-
-
Sarah Leigh
+/., ?/?
3
1
c.-137C>T
r.(=), r.(?)
p.(=)
-
SP1 binding site
-
-
1 more item
-
5-15% LDLR activity when Htz with c.1222G>A, p.(Glu408Lys), FH Algeria-1, FH Osaka, Not tested
ACGS
pathogenic, VUS
g.11200088C>T
g.11089412C>T
FH Albuquerque, LDLR(NM_000527.4):c.-137C>T
-
LDLR_001262
VKGL data sharing initiative Nederland,
2 more items
PubMed: Dedoussis 2003
,
PubMed: Mak 1998
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Sarah Leigh
,
VKGL-NL_AMC
+?/+?
1
1
c.-136C>G
r.(=)
p.(=)
-
SP1 binding site
-
-
1 more item
-
1 more item
ACGS
likely pathogenic
g.11200089C>G
g.11089413C>G
Hobb’s -43C>T
-
LDLR_001260
prediction reduced transcription
PubMed: De Castro-Oros 2011
-
-
Germline
-
0.06 in this study
-
-
-
Sarah Leigh
+/., +?/+?
6
1
c.-136C>T
r.(=), r.(?)
p.(=)
-
SP1 binding site
-
-
1 more item
-
Transcription level of variant reduced to <5% of wt,
1 more item
ACGS
likely pathogenic, pathogenic
g.11200089C>T
g.11089413C>T
Hobb’s -43C>T, LDLR(NM_000527.4):c.-136C>T
-
LDLR_001261
prediction reduced transcription, VKGL data sharing initiative Nederland,
1 more item
PubMed: Fouchier 2005
,
PubMed: Jensen 1996
,
PubMed: Kim 2004
,
PubMed: Koivisto 1994
,
1 more item
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Sarah Leigh
,
VKGL-NL_AMC
?/.
1
_1
c.-135C>A
r.(=)
p.(?)
Disease causing
-
-
-
-
-
-
ACMG
VUS
g.11200090C>A
g.11089414C>A
g.5034C>A
-
LDLR_001906
-
Journal: Banares 2017
-
-
Germline
-
1/33 cases
-
-
-
Virginia Bañares
+/., +?/+, +?/+?, +?/?
5
1
c.-135C>G
r.(=), r.(?)
p.(0), p.(=)
-
SP1 binding site
-
-
1 more item
-
2 more items
ACGS
likely pathogenic, pathogenic
g.11200090C>G
g.11089414C>G
Hobb’s -42C>T; FH Columbia-2, LDLR(NM_000527.4):c.-135C>G
-
LDLR_000003
predicted reduced transcription; On the same allele as c.1185G>C, p.(Val395Val),
2 more items
PubMed: Bourbon 2009
,
PubMed: Hobbs 1992
,
PubMed: Medeiros 2010
,
PubMed: Mozas 2004
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Sarah Leigh
,
VKGL-NL_AMC
?/.
1
1
c.-134C>A
r.(=)
p.(=)
-
-
-
-
-
-
-
-
VUS
g.11200091C>A
g.11089415C>A
-
-
LDLR_002179
-
Journal: Gomez 2017
-
-
Germline/De novo (untested)
-
-
-
-
-
Andrea Gomez
?/.
1
-
c.-122C>T
r.(?)
p.(=)
-
-
-
-
-
-
-
-
VUS
g.11200103C>T
g.11089427C>T
LDLR(NM_000527.4):c.-122C>T
-
LDLR_002042
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+?/+?
2
1
c.-121T>C
r.(=)
p.(=)
-
TATA box/SP1 binding site
-
-
1 more item
-
1 more item
ACGS
likely pathogenic
g.11200104T>C
g.11089428T>C
-
-
LDLR_000002
1 more item
PubMed: Hooper 2012
,
PubMed: Taylor 2010
-
-
Germline
-
-
-
-
-
Sarah Leigh
+?/+?, +?/.
5
1
c.-120C>T
r.(=), r.(?)
p.(=)
-
TATA box/SP1 binding site
-
-
1 more item
-
3% of WT promoter activity (luciferase assay)
ACGS
likely pathogenic
g.11200105C>T
g.11089429C>T
Hobb’s -27C>T, LDLR(NM_000527.4):c.-120C>T
-
LDLR_001115
prediction reduced transcription, VKGL data sharing initiative Nederland,
1 more item
PubMed: Alonso 2009
,
PubMed: Francova 2004
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Sarah Leigh
,
VKGL-NL_AMC
?/+?
1
1
c.-101T>C
r.(=)
p.(=)
-
TATA box
-
-
1 more item
-
1 more item
ACGS
VUS
g.11200124T>C
g.11089448T>C
-
-
LDLR_000001
1 more item
PubMed: Usifo 2012
-
-
Germline
-
-
-
-
-
Sarah Leigh
?/.
1
-
c.-98C>T
r.(?)
p.(=)
-
-
-
-
-
-
-
-
VUS
g.11200127C>T
g.11089451C>T
LDLR(NM_000527.4):c.-98C>T
-
LDLR_001925
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
-?/-?
1
1
c.-88G>A
r.(=)
p.(=)
-
5'UTR
-
-
1 more item
-
Normal levels of transcription (luciferase assay in HEPG2 cells)
ACGS
likely benign
g.11200137G>A
g.11089461G>A
-
-
LDLR_001270
prediction no effect on transcription
PubMed: De Castro-Oros 2011
-
-
Germline
-
0.06 in this study
-
-
-
Sarah Leigh
?/?
1
1
c.-68A>C
r.(=)
p.(=)
-
5'UTR
-
-
1 more item
-
not tested
ACGS
VUS
g.11200157A>C
g.11089481A>C
-
-
LDLR_001121
-
PubMed: Laurie 2004
-
-
Germline
-
-
-
-
-
Sarah Leigh
?/.
1
-
c.-48A>G
r.(?)
p.(=)
-
-
-
-
-
-
-
-
VUS
g.11200177A>G
g.11089501A>G
LDLR(NM_000527.4):c.-48A>G
-
LDLR_002216
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-?/.
1
-
c.-47G>T
r.(?)
p.(=)
-
-
-
-
-
-
-
-
likely benign
g.11200178G>T
-
LDLR(NM_000527.4):c.-47G>T
-
LDLR_002221
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-?/-?
1
1
c.-36T>G
r.(=)
p.(=)
-
5'UTR
-
-
1 more item
-
Normal levels of transcription (luciferase assay in HEPG2 cells)
ACGS
likely benign
g.11200189T>G
g.11089513T>G
-
-
LDLR_001269
prediction no effect on transcription
PubMed: De Castro-Oros 2011
-
-
Germline
-
0.06 in this study
-
-
-
Sarah Leigh
?/?
1
1
c.-23A>C
r.(=)
p.(=)
-
5'UTR
-
-
1 more item
-
not tested
ACGS
VUS
g.11200202A>C
g.11089526A>C
-
-
LDLR_000815
-
PubMed: Mozas 2004
-
-
Germline
-
-
-
-
-
Sarah Leigh
?/.
1
-
c.-22C>T
r.(?)
p.(=)
-
-
-
-
-
-
-
-
VUS
g.11200203C>T
g.11089527C>T
LDLR(NM_000527.4):c.-22C>T
-
LDLR_002181
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
?/?
1
1
c.-22del
r.(=)
p.(=)
-
5'UTR
-
-
1 more item
-
not tested
ACGS
VUS
g.11200203del
g.11089527del
c.-22delC
-
LDLR_001139
1 more item
PubMed: Sozen 2005
-
-
Germline
-
-
-
-
-
Sarah Leigh
-?/.
1
-
c.-17T>C
r.(?)
p.(=)
-
-
-
-
-
-
-
-
likely benign
g.11200208T>C
-
LDLR(NM_000527.4):c.-17T>C
-
LDLR_002262
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
?/?
1
1
c.-14C>A
r.(=)
p.(=)
-
5'UTR
-
-
1 more item
-
not tested
ACGS
VUS
g.11200211C>A
g.11089535C>A
-
-
LDLR_001265
-
PubMed: Day 1997
-
-
Germline
-
-
-
-
-
Sarah Leigh
-?/?
1
1
c.-13A>G
r.(=)
p.(=)
-
5'UTR
-
-
1 more item
-
1 more item
ACGS
likely benign
g.11200212A>G
g.11089536A>G
-
-
LDLR_000004
prediction no effect on transcription
PubMed: Medeiros 2010
-
-
Germline
-
-
-
-
-
Sarah Leigh
-?/.
1
-
c.-7T>A
r.(?)
p.(=)
-
-
-
-
-
-
-
-
likely benign
g.11200218T>A
g.11089542T>A
LDLR(NM_000527.4):c.-7T>A
-
LDLR_001926
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
?/?
1
1
c.-5C>T
r.(=)
p.(=)
-
5'UTR
-
-
1 more item
-
not tested
ACGS
VUS
g.11200220C>T
g.11089544C>T
-
-
LDLR_001026
-
PubMed: Fouchier 2005
-
-
Germline
-
-
-
-
-
Sarah Leigh
+?/+?
3
1
c.1A>C
r.(?)
p.0?
disease causing
signal peptide
PPII HumDiv benign, 0.167; HumVar benign, 0.354
Not tolerated; SIFT2 Not tolerated
0.175; (Ch, Rh, B, M, Ra, H, X, S)
-
-
ACGS
likely pathogenic
g.11200225A>C
g.11089549A>C
-
-
LDLR_000356
1 more item
PubMed: Chaves 2001
,
PubMed: Fouchier 2005
,
PubMed: Tosi 2007
-
-
Germline
-
not in ExAC, May 2015
-
-
-
Sarah Leigh
+/., +?/+?
4
1
c.1A>G
r.(?)
p.(Met1?), p.0?
disease causing
signal peptide
PPII HumDiv benign, 0.323; HumVar benign, 0.354
Not tolerated; SIFT2 Not tolerated
0.175; (Ch, Rh, B, M, Ra, H, X, S)
-
-
ACGS
likely pathogenic, pathogenic
g.11200225A>G
g.11089549A>G
LDLR(NM_000527.4):c.1A>G (p.M1?)
-
LDLR_000328
VKGL data sharing initiative Nederland,
1 more item
PubMed: Bourbon 2008
,
PubMed: Lombardi 1997
,
PubMed: Nauck 2001
-
-
CLASSIFICATION record, Germline
-
not in ExAC, May 2015
-
-
-
Sarah Leigh
,
VKGL-NL_AMC
+/., +?/+?
2
1
c.1A>T
r.(?)
p.(Met1?), p.0?
disease causing
signal peptide
PPII HumDiv benign, 0.167; HumVar benign, 0.354
Not tolerated; SIFT2 Not tolerated
0.175; (Ch, Rh, B, M, Ra, H, X, S)
-
-
ACGS
likely pathogenic, pathogenic
g.11200225A>T
g.11089549A>T
LDLR(NM_000527.4):c.1A>T (p.M1?)
-
LDLR_000445
VKGL data sharing initiative Nederland,
1 more item
PubMed: Langenhoven 1996
-
-
CLASSIFICATION record, Germline
-
not in ExAC, May 2015
-
-
-
Sarah Leigh
,
VKGL-NL_AMC
+/+
2
_1_2i
c.[(?_-187)_(190+1_191-1)del;(1060+1_1061-1)_(1845+1_1846-1)del]
r.(?)
p.0?
-
Promoter - exon 2 & exons 8-12
-
-
-
-
-
ACGS
pathogenic
g.[11200038_11211021del;11222190_11227674del]
-
c.[-187-?_190+?del;1061-?_1845+?del]
-
LDLR_000000
2 more items
PubMed: Bourbon 2008
,
PubMed: Marduel 2010
-
-
Germline
-
-
-
-
-
Sarah Leigh
+/.
1
-
c.2T>C
r.(?)
p.(Met1?)
-
-
-
-
-
-
-
-
pathogenic
g.11200226T>C
g.11089550T>C
LDLR(NM_000527.4):c.2T>C (p.M1?)
-
LDLR_001927
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+?/?
1
1
c.3G>T
r.(?)
p.0?
disease causing
signal peptide
PPII HumDiv possibly damaging, 0.525; HumVar possibly damaging, 0.48
Not tolerated; SIFT2 Not tolerated
0.175; (Ch, Rh, B, M, Ra, H, X, S)
-
-
ACGS
likely pathogenic
g.11200227G>T
g.11089551G>T
-
-
LDLR_000316
p.(Met1Ile), normal translation from this codon would not occur
Lucac Tichy db submission
-
-
Germline
-
1/3900 in this study. not in ExAC, May 2015
-
-
-
Sarah Leigh
-?/-?
1
1
c.4G>A
r.(?)
p.(Gly2Arg)
polymorphism
signal peptide
PPII HumDiv benign, 0; HumVar benign, 0
Tolerated; SIFT2 Not tolerated
0.113; (Rh)
-
-
ACGS
likely benign
g.11200228G>A
g.11089552G>A
G-20R
-
LDLR_001027
-
PubMed: Fouchier 2005
-
rs5931
Germline
-
not in ExAC, May 2015
-
-
-
Sarah Leigh
-?/-?
1
1
c.4G>C
r.(?)
p.(Gly2Arg)
polymorphism
signal peptide
PPII HumDiv benign, 0; HumVar benign, 0
Tolerated; SIFT2 Not tolerated
0.113; (Rh)
-
-
ACGS
likely benign
g.11200228G>C
g.11089552G>C
G-20R
-
LDLR_001001
-
PubMed: Salazar 2002
-
rs5931
Germline
-
0.00001731 ExAC, May 2015
-
-
-
Sarah Leigh
+/+
1
1
c.6del
r.(?)
p.(Trp4Glyfs*202)
-
signal peptide
-
-
-
-
-
ACGS
pathogenic
g.11200230del
g.11089554del
c.6delG, G-20fsX214
-
LDLR_001825
1 more item
PubMed: Day 1997
-
-
Germline
-
-
-
-
-
Sarah Leigh
+/+
3
1
c.9del
r.(?)
p.(Trp4Glyfs*202)
-
signal peptide
-
-
-
-
<2% LDLR activity when Htz with unknown FH allele
ACGS
pathogenic
g.11200233del
g.11089557del
c.9delC, P-19fsX202; FH Dallas-1, c.9delC, P-19fsX203; FH Dallas-1
-
LDLR_001899
predicted trucated protein; 1bp deletion (C in a run of 3 Cs),
2 more items
PubMed: Hobbs 1992
,
PubMed: Mozas 2004
-
-
Germline
-
-
-
-
-
Sarah Leigh
+/+
3
1
c.11G>A
r.(?)
p.(Trp4*)
-
signal peptide
-
-
-
-
<2% LDLR activity in Hmz
ACGS
pathogenic
g.11200235G>A
g.11089559G>A
W-18X; FH Columbia-1
-
LDLR_001492
prediction no protein
PubMed: Cenarro 1998
,
PubMed: Hobbs 1992
,
PubMed: Robles-Osorio 2006
-
-
Germline
-
not in ExAC, August 2015
-
-
-
Sarah Leigh
+/+
3
1
c.12G>A
r.(?)
p.(Trp4*)
-
signal peptide
-
-
-
-
<2% LDLR activity when Htz with c.2012delC, p.(Leu672*), FH Nanjing-2
ACGS
pathogenic
g.11200236G>A
g.11089560G>A
W-18X ; FH Nanjing-1
-
LDLR_000357
prediction no protein,
1 more item
PubMed: Cenarro 1998
,
PubMed: Hobbs 1992
,
PubMed: Robles-Osorio 2006
-
-
Germline
-
not in ExAC, August 2015
-
-
-
Sarah Leigh
+/.
1
-
c.25_29del
r.(?)
p.(Arg9Aspfs*41)
-
-
-
-
-
-
-
-
pathogenic
g.11200249_11200253del
-
LDLR(NM_000527.4):c.25_29delCGCTG (p.R9Dfs*41)
-
LDLR_002263
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+?/+?
1
1
c.28T>A
r.(?)
p.(Trp10Arg)
polymorphism
signal peptide
PPII HumDiv possibly damaging, 0.836; HumVar possibly damaging, 0.549
Not tolerated; SIFT2 Not tolerated
0.114; (Ch, Rh, B, M, Ra, H, Ck)
-
40% LDLR activity in fibroblasts of de novo Htz
ACGS
likely pathogenic
g.11200252T>A
g.11089576T>A
W-12R; FH Enna
-
LDLR_001681
1 more item
PubMed: Cassanelli 1998
-
-
Germline
-
not in ExAC, May 2015
-
-
-
Sarah Leigh
+/., +?/+?, +?/.
3
1
c.28T>C
r.(?)
p.(Trp10Arg)
polymorphism
signal peptide
PPII HumDiv possibly damaging, 0.836; HumVar possibly damaging, 0.549
Not tolerated; SIFT2 Not tolerated
0.114; (Ch, Rh, B, M, Ra, H, Ck)
-
reduced LDLR activity
ACGS
likely pathogenic, pathogenic
g.11200252T>C
g.11089576T>C
LDLR(NM_000527.4):c.28T>C (p.W10R), W-12R
-
LDLR_000260
VKGL data sharing initiative Nederland,
1 more item
PubMed: Fouchier 2005
-
-
CLASSIFICATION record, Germline
-
not in ExAC, May 2015
-
-
-
Sarah Leigh
,
VKGL-NL_Groningen
,
VKGL-NL_AMC
+/+
1
1
c.28_38del
r.(?)
p.(Trp10Leufs*38)
-
signal peptide
-
-
-
-
-
ACGS
pathogenic
g.11200252_11200262del
g.11089576_11089586del
p.(Trp-12Leufs*38)
-
LDLR_001677
predicted trucated protein; 11bp deletion of CTGGACCGTCG
PubMed: Guardamagna 2009
-
-
Germline
-
not in ExAC, September 2015
-
-
-
Sarah Leigh
+/.
1
-
c.29G>A
r.(?)
p.(Trp10Ter)
-
-
-
-
-
-
-
-
pathogenic
g.11200253G>A
g.11089577G>A
LDLR(NM_000527.4):c.29G>A (p.W10*)
-
LDLR_002043
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/+
1
1
c.33_36dup
r.(?)
p.(Ala13Argfs*40)
-
signal peptide
-
-
-
-
-
ACGS
pathogenic
g.11200257_11200260dup
g.11089581_11089584dup
c.33_36dupCGTC, ({0}Ala-9Argfs*40)
-
LDLR_001703
prediction truncated protein
PubMed: Alonso 2009
-
-
Germline
-
not in ExAC, September 2015
-
-
-
Sarah Leigh
-?/.
1
-
c.38C>T
r.(?)
p.(Ala13Val)
-
-
-
-
-
-
-
-
likely benign
g.11200262C>T
g.11089586C>T
LDLR(NM_000527.4):c.38C>T (p.A13V)
-
LDLR_001928
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+/+
1
1
c.41del
r.(?)
p.(Leu14Cysfs*192)
-
signal peptide
-
-
-
-
-
ACGS
pathogenic
g.11200265del
g.11089589del
c.41delT, ({0}Leu-8Cysfs*192)
-
LDLR_000011
prediction truncated protein
PubMed: Whittall 2010
-
-
Germline
-
-
-
-
-
Sarah Leigh
+/+, +/.
2
1
c.41dup
r.(?)
p.(Leu14Phefs*38), p.(Leu14PhefsTer38)
-
signal peptide
-
-
-
-
-
ACGS
pathogenic
g.11200265dup
g.11089589dup
c.41_42insT, L-8FfsX38, LDLR(NM_000527.4):c.41dupT (p.L14Ffs*38)
-
LDLR_001132
prediction truncated protein, VKGL data sharing initiative Nederland
PubMed: Sozen 2005
-
-
CLASSIFICATION record, Germline
-
-
-
-
-
Sarah Leigh
,
VKGL-NL_AMC
-?/.
1
-
c.42G>T
r.(?)
p.(Leu14Phe)
-
-
-
-
-
-
-
-
likely benign
g.11200266G>T
g.11089590G>T
LDLR(NM_000527.4):c.42G>T (p.L14F)
-
LDLR_001929
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
+?/+?
1
1
c.44T>A
r.(?)
p.(Leu15His)
disease causing
signal peptide
PPII HumDiv probably damaging 0.992; HumVar possibly damaging, 0.770
Not tolerated; SIFT2 Not tolerated
0.174; (Ch, Rh, B, M, Ra, H, Rb, X, S)
-
-
ACGS
likely pathogenic
g.11200268T>A
g.11089592T>A
L-7P
-
LDLR_001736
-
PubMed: Leren 2004
-
-
Germline
-
not in ExAC, March 2016
-
-
-
Sarah Leigh
?/?
1
1
c.44T>C
r.(?)
p.(Leu15Pro)
disease causing
signal peptide
PPII HumDiv benign, 0.005; HumVar benign, 0.009
Not tolerated; SIFT2 Tolerated
0.174; (Ch, Rh, B, M, Ra, H, Rb, X, S)
-
-
ACGS
VUS
g.11200268T>C
g.11089592T>C
L-7P
-
LDLR_001011
-
PubMed: Lind 2002
-
-
Germline
-
not in ExAC, May 2015
-
-
-
Sarah Leigh
+?/+?
1
1
c.47T>C
r.(?)
p.(Leu16Pro)
disease causing
signal peptide
PPII HumDiv possibly damaging, 0.940; HumVar possibly damaging, 0.713
Tolerated; SIFT2 Not tolerated
0.152; (Ch, Rh, D, M, Ra, H, Z)
-
-
ACGS
likely pathogenic
g.11200271T>C
g.11089595T>C
L-6P
-
LDLR_001743
-
PubMed: Alonso 2009
-
-
Germline
-
not in ExAC, August 2015
-
-
-
Sarah Leigh
-/-
1
1
c.48C>A
r.(=)
p.(=)
-
signal peptide
-
-
Ch, Rh, D, M, Ra, H, Z
-
-
ACGS
benign
g.11200272C>A
g.11089596C>A
L-6L
-
LDLR_001205
predicted silent; p.(Leu16=) Rare variant
PubMed: Ekstrom 1995
-
rs565675103
Germline
-
0.00001880 (ExAC May 2015)
-
-
-
Sarah Leigh
?/?
1
1
c.56C>A
r.(?)
p.(Ala19Glu)
polymorphism
signal peptide
PPII HumDiv possibly damaging, 0.646; HumVar benign, 0.183
Not tolerated; SIFT2 Not tolerated
0.196; (Ch, Rh, M, Ra, H, Rb)
-
-
ACGS
VUS
g.11200280C>A
g.11089604C>A
A-3E
-
LDLR_000401
-
PubMed: Shin 2000
-
-
Germline
-
not in ExAC, May 2015
-
-
-
Sarah Leigh
?/-?
1
1
c.56C>T
r.(?)
p.(Ala19Val)
polymorphism
signal peptide
PPII HumDiv benign, 0.013; HumVar benign, 0.003
Not tolerated; SIFT2 Not tolerated
0.196; (Ch, Rh, M, Ra, H, Rb)
-
-
ACGS
VUS
g.11200280C>T
g.11089604C>T
A-3V
-
LDLR_000012
-
PubMed: Usifo 2012
-
-
Germline
-
not in ExAC, May 2015
-
-
-
Sarah Leigh
-?/+?, -?/-?, -?/., -?/?
11
1
c.58G>A
r.(?)
p.(Gly20Arg)
polymorphism
signal peptide
PPII HumDiv benign, 0.12; HumVar benign, 0.099
Tolerated; SIFT2 Tolerated
0.186; (Ch, M, Ra, H, Rb)
-
-
ACGS
likely benign
g.11200282G>A
g.11089606G>A
G-2R, LDLR(NM_000527.4):c.58G>A (p.G20R)
-
LDLR_000013
Corrected after personal communication with author. Non-polar>Charged(+)-polar,
2 more items
PubMed: Alonso 2009
,
PubMed: Amsellem 2002
,
PubMed: Bertolini 2013
,
PubMed: Chmara 2010
,
6 more items
-
rs147509697
CLASSIFICATION record, Germline
-
0.001046 ExAC, May 2015,
1 more item
-
-
-
Sarah Leigh
,
VKGL-NL_AMC
+/+
1
1
c.64del
r.(?)
p.(Ala22Glnfs*184)
-
-
-
-
-
-
-
ACGS
pathogenic
g.11200288del
g.11089612del
c.64delG, ({0}Ala1Glnfs*184)
-
LDLR_001786
predicted trucated protein; Segregation reported in affected family members in this article
PubMed: Chiou 2012
-
-
Germline
-
-
-
-
-
Sarah Leigh
+?/+?
1
1i
c.67+2T>A
r.spl
p.?
-
Intron 1
-
-
-
-
-
ACGS
likely pathogenic
g.11200293T>A
g.11089617T>A
-
-
LDLR_000877
-
PubMed: Amsellem 2002
-
-
Germline
-
not in ExAC, June 2015
-
-
-
Sarah Leigh
-/.
1
-
c.67+18C>A
r.(=)
p.(=)
-
-
-
-
-
-
-
-
benign
g.11200309C>A
g.11089633C>A
LDLR(NM_000527.4):c.67+18C>A
-
LDLR_001930
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
?/.
1
-
c.67+121C>T
r.(=)
p.(=)
-
-
-
-
-
-
-
-
VUS
g.11200412C>T
g.11089736C>T
LDLR(NM_000527.4):c.67+121C>T
-
LDLR_002044
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-?/.
1
-
c.67+184C>G
r.(=)
p.(=)
-
-
-
-
-
-
-
-
likely benign
g.11200475C>G
-
LDLR(NM_000527.4):c.67+184C>G
-
LDLR_002241
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-/.
1
-
c.67+223C>T
r.(=)
p.(=)
-
-
-
-
-
-
-
-
benign
g.11200514C>T
g.11089838C>T
LDLR(NM_000527.4):c.67+223C>T
-
LDLR_002045
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-/.
1
-
c.67+1700del
r.(=)
p.(=)
-
-
-
-
-
-
-
-
benign
g.11201991del
-
LDLR(NM_000527.4):c.67+1700delT
-
LDLR_002222
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
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