VCV000250970.4 - ClinVar

NM_000527.5(LDLR):c.4G>A (p.Gly2Arg)

Germline

Top reviewed classifications are shown here.

Submission summary:

3 submissions

3 submitters

1 condition

Reviewed by expert panel

Uncertain significance

Mar 2022 by ClinGen Famili… FDA Recognized Database

for Hypercholesterolemia, familial, 1

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000527.5(LDLR):c.4G>A (p.Gly2Arg)

Variation ID: 250970 Accession: VCV000250970.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 19p13.2 19: 11089552 (GRCh38) [ NCBI UCSC ] 19: 11200228 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Jul 29, 2016	May 7, 2022	Mar 8, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_000527.5:c.4G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000518.1:p.Gly2Arg	missense
NM_001195798.2:c.4G>A	NP_001182727.1:p.Gly2Arg	missense
NM_001195799.2:c.4G>A	NP_001182728.1:p.Gly2Arg	missense
NM_001195800.2:c.4G>A	NP_001182729.1:p.Gly2Arg	missense
NM_001195803.2:c.4G>A	NP_001182732.1:p.Gly2Arg	missense
NR_163945.1:n.108C>T		non-coding transcript variant
NC_000019.10:g.11089552G>A
NC_000019.9:g.11200228G>A
NG_009060.1:g.5172G>A
LRG_274:g.5172G>A
LRG_274t1:c.4G>A	LRG_274p1:p.Gly2Arg
	P01130:p.Gly2Arg

... more HGVS ... less HGVS

Protein change

G2R

Other names

NM_000527.5(LDLR):c.4G>A

Canonical SPDI

NC_000019.10:11089551:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA10584722 LDLR-LOVD, British Heart Foundation: LDLR_001027 UniProtKB: P01130#VAR_011862 dbSNP: rs5931 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
LDLR		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	4076	4352
LDLR-AS1	-	-	-	GRCh38	-	204

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Hypercholesterolemia, familial, 1	Uncertain significance (3)	reviewed by expert panel	Mar 8, 2022	RCV000238070.5

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Mar 08, 2022)	reviewed by expert panel (ClinGen FH ACMG Specifications v1-2) Method: curation	Hypercholesterolemia, familial, 1 (Semidominant inheritance) Affected status: unknown Allele origin: germline	ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel FDA Recognized Database Accession: SCV002506406.1 First in ClinVar: May 07, 2022 Last updated: May 07, 2022	Other databases https://erepo.clinicalgenome.org… https://erepo.clinicalgenome.org/evrepo/ui/interpretation/0ddd220f-6fa7-470e-a89c-bc65694949a5 Comment: NM_000527.5(LDLR):c.4G>A (p.Gly2Arg) variant is classified as uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence code PM2 as defined by the ClinGen Familial … (more) NM_000527.5(LDLR):c.4G>A (p.Gly2Arg) variant is classified as uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence code PM2 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: PM2 - Variant is absent from gnomAD (gnomAD v2.1.1). (less)
Likely benign (Mar 25, 2016)	criteria provided, single submitter (ACGS Guidelines, 2013) Method: literature only	Familial hypercholesterolemia Affected status: yes Allele origin: germline	LDLR-LOVD, British Heart Foundation Accession: SCV000294409.2 First in ClinVar: Jul 29, 2016 Last updated: May 30, 2018	Publications: PubMed (1) PubMed: 16250003 Number of individuals with the variant: 1
Pathogenic (-)	no assertion criteria provided Method: research	Familial hypercholesterolemia Affected status: unknown Allele origin: germline	Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum Accession: SCV000605994.1 First in ClinVar: Jul 29, 2016 Last updated: Jul 29, 2016

Comment:

NM_000527.5(LDLR):c.4G>A (p.Gly2Arg) variant is classified as uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence code PM2 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: PM2 - Variant is absent from gnomAD (gnomAD v2.1.1).

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Update of the molecular basis of familial hypercholesterolemia in The Netherlands.	Fouchier SW	Human mutation	2005	PMID: 16250003
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/0ddd220f-6fa7-470e-a89c-bc65694949a5	-	-	-	-

Text-mined citations for rs5931 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 06, 2023

ClinVar Genomic variation as it relates to human health

NM_000527.5(LDLR):c.4G>A (p.Gly2Arg)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs5931 ...