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NM_000090.4(COL3A1):c.1744G>A (p.Gly582Ser) AND COL3A1-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 28, 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:
RCV004528122.1

Allele description [Variation Report for NM_000090.4(COL3A1):c.1744G>A (p.Gly582Ser)]

NM_000090.4(COL3A1):c.1744G>A (p.Gly582Ser)

Gene:
COL3A1:collagen type III alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q32.2
Genomic location:
Preferred name:
NM_000090.4(COL3A1):c.1744G>A (p.Gly582Ser)
Other names:
G415S; p.G582S:GGT>AGT
HGVS:
  • NC_000002.12:g.188996479G>A
  • NG_007404.1:g.27107G>A
  • NM_000090.4:c.1744G>AMANE SELECT
  • NP_000081.1:p.Gly582Ser
  • NP_000081.2:p.Gly582Ser
  • LRG_3t1:c.1744G>A
  • LRG_3:g.27107G>A
  • LRG_3p1:p.Gly582Ser
  • NC_000002.11:g.189861205G>A
  • NM_000090.3:c.1744G>A
  • P02461:p.Gly582Ser
Protein change:
GLY415SER
Links:
UniProtKB: P02461#VAR_001774; OMIM: 120180.0024; dbSNP: rs121912923
NCBI 1000 Genomes Browser:
rs121912923
Molecular consequence:
  • NM_000090.4:c.1744G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
COL3A1-related disorder
Synonyms:
COL3A1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004111005PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Jul 28, 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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004111005.1

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

Description

The COL3A1 c.1744G>A variant is predicted to result in the amino acid substitution p.Gly582Ser. This variant was reported in individuals with Ehlers-Danlos syndrome IV (vascular type) (Anderson et al. 1997. PubMed ID: 8990011, reported as p.Gly415Ser; Legrand et al. 2018. PubMed ID: 30474650; Henneton et al. 2019. PubMed ID: 30919682; Pepin et al. 2000. PubMed ID: 10706896, reported as Gly415Ser). This variant was also reported as pathogenic in another patient with aneurysm (Weerakkody et al. 2018. PubMed ID: 29543232). In addition, a different variant affecting the same amino acid residue (p.Gly582SArg) was reported to be pathogenic for Ehlers-Danlos Syndrome (Kerwin et al. 2008. PubMed ID: 18043893). This variant impacts a glycine residue of the highly conserved collagen triple helical domain (Gly-X-Y) where Gly substitutions are expected to be pathogenic. This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic.

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

Last Updated: Jun 2, 2024