NM_000821.7(GGCX):c.1465G>A (p.Val489Met) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 9, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV002600781.3

Allele description [Variation Report for NM_000821.7(GGCX):c.1465G>A (p.Val489Met)]

NM_000821.7(GGCX):c.1465G>A (p.Val489Met)

Gene:

GGCX:gamma-glutamyl carboxylase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p11.2

Genomic location:

Preferred name:

NM_000821.7(GGCX):c.1465G>A (p.Val489Met)

HGVS:

NC_000002.12:g.85551956C>T
NG_011811.2:g.14579G>A
NM_000821.7:c.1465G>AMANE SELECT
NM_001142269.4:c.1294G>A
NP_000812.2:p.Val489Met
NP_001135741.1:p.Val432Met
LRG_592t1:c.1465G>A
LRG_592:g.14579G>A
LRG_592p1:p.Val489Met
NC_000002.11:g.85779079C>T

Protein change:

V432M

Molecular consequence:

NM_000821.7:c.1465G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142269.4:c.1294G>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
SCV002941559	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 9, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 31727138, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002941559

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 9, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Novel risk genes and mechanisms implicated by exome sequencing of 2572 individuals with pulmonary arterial hypertension.

Zhu N, Pauciulo MW, Welch CL, Lutz KA, Coleman AW, Gonzaga-Jauregui C, Wang J, Grimes JM, Martin LJ, He H; PAH Biobank Enrolling Centers’ Investigators., Shen Y, Chung WK, Nichols WC.

Genome Med. 2019 Nov 14;11(1):69. doi: 10.1186/s13073-019-0685-z. Erratum in: Genome Med. 2022 Feb 7;14(1):12. doi: 10.1186/s13073-022-01014-0.

PubMed [citation]

PMID:: 31727138
PMCID:: PMC6857288

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002941559.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This missense change has been observed in individual(s) with pulmonary arterial hypertension (PMID: 31727138). This variant is present in population databases (rs375186088, gnomAD 0.02%). This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 489 of the GGCX protein (p.Val489Met).

#	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

Last Updated: Sep 29, 2024

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