VCV000006283.4 - ClinVar

NM_002335.4(LRP5):c.640G>A (p.Ala214Thr)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_002335.4(LRP5):c.640G>A (p.Ala214Thr)

Variation ID: 6283 Accession: VCV000006283.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 11q13.2 11: 68357801 (GRCh38) [ NCBI UCSC ] 11: 68125269 (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	Apr 4, 2013	May 14, 2021	Dec 12, 2018

HGVS

Nucleotide	Protein	Molecular consequence
NM_002335.4:c.640G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_002326.2:p.Ala214Thr	missense
NM_001291902.2:c.-1126G>A		5 prime UTR
NC_000011.10:g.68357801G>A
NC_000011.9:g.68125269G>A
NG_015835.2:g.50162G>A
	O75197:p.Ala214Thr

... more HGVS ... less HGVS

Protein change

A214T

Other names

Canonical SPDI

NC_000011.10:68357800: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: CA118098 UniProtKB: O75197#VAR_021810 OMIM: 603506.0016 dbSNP: rs121908671 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.
LRP5		Some evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	2064	2081

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.
Worth disease	Pathogenic (1)	no assertion criteria provided	Mar 1, 2003	RCV000006663.3
Autosomal dominant osteopetrosis 1	Pathogenic (1)	no assertion criteria provided	Dec 12, 2018	RCV000786921.2

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.
Pathogenic (Dec 12, 2018)	no assertion criteria provided Method: clinical testing	Autosomal dominant osteopetrosis 1 Affected status: yes Allele origin: germline	Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare Accession: SCV000925822.1 First in ClinVar: Jul 14, 2019 Last updated: Jul 14, 2019
Pathogenic (Mar 01, 2003)	no assertion criteria provided Method: literature only	ENDOSTEAL HYPEROSTOSIS, AUTOSOMAL DOMINANT Affected status: not provided Allele origin: germline	OMIM Accession: SCV000026846.2 First in ClinVar: Apr 04, 2013 Last updated: May 14, 2021	Publications: PubMed (2) PubMed: 1002767‚ 12579474 Comment on evidence: In a family from Portland, Oregon (kindred C) with autosomal dominant endosteal hyperostosis (144750), originally described by Beals et al. (2001), Van Wesenbeeck et al. … (more) In a family from Portland, Oregon (kindred C) with autosomal dominant endosteal hyperostosis (144750), originally described by Beals et al. (2001), Van Wesenbeeck et al. (2003) found a 640G-A transition in exon 3 of the LRP5 gene, resulting in an ala214-to-thr (A214T) mutation. A different mutation involving the same codon (A214V; 603506.0017) was identified in another family (kindred E) diagnosed with a similar phenotype of increased bone density. (less)

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.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Six novel missense mutations in the LDL receptor-related protein 5 (LRP5) gene in different conditions with an increased bone density.	Van Wesenbeeck L	American journal of human genetics	2003	PMID: 12579474
Endosteal hyperostosis.	Beals RK	The Journal of bone and joint surgery. American volume	1976	PMID: 1002767

Text-mined citations for rs121908671 ...

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 Mar 05, 2023

ClinVar Genomic variation as it relates to human health

NM_002335.4(LRP5):c.640G>A (p.Ala214Thr)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs121908671 ...