NM_001171.6(ABCC6):c.2974G>C (p.Gly992Arg) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 11, 2023
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:: RCV003558407.2

Allele description [Variation Report for NM_001171.6(ABCC6):c.2974G>C (p.Gly992Arg)]

NM_001171.6(ABCC6):c.2974G>C (p.Gly992Arg)

Gene:

ABCC6:ATP binding cassette subfamily C member 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.11

Genomic location:

Preferred name:

NM_001171.6(ABCC6):c.2974G>C (p.Gly992Arg)

HGVS:

NC_000016.10:g.16169667C>G
NG_007558.3:g.58951G>C
NM_001171.6:c.2974G>CMANE SELECT
NM_001351800.1:c.2632G>C
NP_001162.4:p.Gly992Arg
NP_001162.5:p.Gly992Arg
NP_001338729.1:p.Gly878Arg
LRG_1115t1:c.2974G>C
LRG_1115:g.58951G>C
LRG_1115p1:p.Gly992Arg
NC_000016.9:g.16263524C>G
NG_007558.2:g.58805G>C
NM_001171.5:c.2974G>C
NR_147784.1:n.2836G>C

Protein change:

G878R

Links:

dbSNP: rs72657692

NCBI 1000 Genomes Browser:

rs72657692

Molecular consequence:

NM_001171.6:c.2974G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001351800.1:c.2632G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_147784.1:n.2836G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV004296403	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 11, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 15894595, 30805891, 32873932, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004296403

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 11, 2023)

germline

clinical testing

PubMed (4)
[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

Pseudoxanthoma elasticum: a clinical, pathophysiological and genetic update including 11 novel ABCC6 mutations.

Chassaing N, Martin L, Calvas P, Le Bert M, Hovnanian A.

J Med Genet. 2005 Dec;42(12):881-92. Epub 2005 May 13. Review.

PubMed [citation]

PMID:: 15894595
PMCID:: PMC1735972

Whole exome sequencing identified three ABCC6 variants in two Pakistani families with pseudoxanthoma elasticum phenotype.

Khan FF, Erfan M, Kanwal N, Naeem M.

Mol Biol Rep. 2019 Feb;46(1):1363-1368. doi: 10.1007/s11033-018-04581-x. Epub 2019 Feb 25.

PubMed [citation]

PMID:: 30805891

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004296403.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ABCC6 protein function. ClinVar contains an entry for this variant (Variation ID: 433299). This variant is also known as 2965G->C. This missense change has been observed in individuals with pseudoxanthoma elasticum (PMID: 15894595, 30805891, 32873932). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 992 of the ABCC6 protein (p.Gly992Arg).

#	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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