U.S. flag

An official website of the United States government

NM_000393.5(COL5A2):c.1960G>A (p.Gly654Ser) AND Ehlers-Danlos syndrome, classic type, 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 3, 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:
RCV001925920.4

Allele description [Variation Report for NM_000393.5(COL5A2):c.1960G>A (p.Gly654Ser)]

NM_000393.5(COL5A2):c.1960G>A (p.Gly654Ser)

Gene:
COL5A2:collagen type V alpha 2 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q32.2
Genomic location:
Preferred name:
NM_000393.5(COL5A2):c.1960G>A (p.Gly654Ser)
HGVS:
  • NC_000002.12:g.189062882C>T
  • NG_011799.3:g.167420G>A
  • NM_000393.3:c.1960G>A
  • NM_000393.5:c.1960G>AMANE SELECT
  • NP_000384.2:p.Gly654Ser
  • LRG_738t1:c.1960G>A
  • LRG_738:g.167420G>A
  • LRG_738p1:p.Gly654Ser
  • NC_000002.11:g.189927608C>T
  • NG_011799.2:g.121998G>A
  • NM_000393.5:c.1960G>A
Protein change:
G654S
Links:
dbSNP: rs773726323
NCBI 1000 Genomes Browser:
rs773726323
Molecular consequence:
  • NM_000393.5:c.1960G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Ehlers-Danlos syndrome, classic type, 1 (EDSCL1)
Synonyms:
EHLERS-DANLOS SYNDROME, GRAVIS TYPE; EHLERS-DANLOS SYNDROME, SEVERE CLASSIC TYPE; Ehlers-Danlos syndrome, type 1; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0019567; MedGen: C0268335; OMIM: 130000

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002177742Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 3, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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, SCV002177742.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

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. 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 COL5A2 protein function. ClinVar contains an entry for this variant (Variation ID: 1413406). This variant has not been reported in the literature in individuals affected with COL5A2-related conditions. This variant is present in population databases (rs773726323, gnomAD 0.003%). This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 654 of the COL5A2 protein (p.Gly654Ser).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024