NM_002335.4(LRP5):c.1999G>A (p.Val667Met) AND not provided

Germline classification:: Benign/Likely benign (6 submissions)
Last evaluated:: Jan 31, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000086953.11

Allele description [Variation Report for NM_002335.4(LRP5):c.1999G>A (p.Val667Met)]

NM_002335.4(LRP5):c.1999G>A (p.Val667Met)

Gene:

LRP5:LDL receptor related protein 5 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.2

Genomic location:

Preferred name:

NM_002335.4(LRP5):c.1999G>A (p.Val667Met)

HGVS:

NC_000011.10:g.68406721G>A
NG_015835.2:g.99082G>A
NM_001291902.2:c.256G>A
NM_002335.4:c.1999G>AMANE SELECT
NP_001278831.1:p.Val86Met
NP_002326.2:p.Val667Met
NC_000011.9:g.68174189G>A
NG_015835.1:g.99082G>A
NM_002335.2:c.1999G>A
NM_002335.3:c.1999G>A
O75197:p.Val667Met

Protein change:

V667M; VAL667MET

Links:

UniProtKB: O75197#VAR_021816; OMIM: 603506.0009; dbSNP: rs4988321

NCBI 1000 Genomes Browser:

rs4988321

Molecular consequence:

NM_001291902.2:c.256G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002335.4:c.1999G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000119205	NEI Ophthalmic Genomics Laboratory, National Institutes of Health	no classification provided	not provided	not provided	not provided
SCV001144464	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Dec 6, 2018)	germline	clinical testing	PubMed (21) [See all records that cite these PMIDs] 11719191, 12579474, 15024691, 15077203, 15201508, 15619672, 15767861, 15777745, 15824851, 15824861, 15850991, 16679074, 17137849, 17202888, 17223614, 17306638, 17307038, 18058054, 18349089, 18588671, 26467025
SCV001731472	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001756828	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Mar 3, 2015)	germline	clinical testing	Citation Link,
SCV001808065	Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV005218822	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing, not provided
not provided	not provided	not provided	not provided	not provided	not provided	1	not provided	literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Gong Y, Slee RB, Fukai N, Rawadi G, Roman-Roman S, Reginato AM, Wang H, Cundy T, Glorieux FH, Lev D, Zacharin M, Oexle K, Marcelino J, Suwairi W, Heeger S, Sabatakos G, Apte S, Adkins WN, Allgrove J, Arslan-Kirchner M, Batch JA, Beighton P, et al.

Cell. 2001 Nov 16;107(4):513-23.

PubMed [citation]

PMID:: 11719191

Six novel missense mutations in the LDL receptor-related protein 5 (LRP5) gene in different conditions with an increased bone density.

Van Wesenbeeck L, Cleiren E, Gram J, Beals RK, Bénichou O, Scopelliti D, Key L, Renton T, Bartels C, Gong Y, Warman ML, De Vernejoul MC, Bollerslev J, Van Hul W.

Am J Hum Genet. 2003 Mar;72(3):763-71. Epub 2003 Feb 10.

PubMed [citation]

PMID:: 12579474
PMCID:: PMC1180253

See all PubMed Citations (23)

Details of each submission

From NEI Ophthalmic Genomics Laboratory, National Institutes of Health, SCV000119205.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	not provided	not provided	1	not provided	not provided		not provided	not provided	not provided	not provided

From Athena Diagnostics, SCV001144464.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (21)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001731472.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV001756828.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is associated with the following publications: (PMID: 30283887, 28222408, 15077203, 18026682, 18349089, 22025579, 18058054, 11719191, 17307038, 22511589, 21116122)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV001808065.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005218822.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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