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NM_000090.4(COL3A1):c.1714C>T (p.Arg572Ter) AND Ehlers-Danlos syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 11, 2019
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:
RCV004017969.1

Allele description [Variation Report for NM_000090.4(COL3A1):c.1714C>T (p.Arg572Ter)]

NM_000090.4(COL3A1):c.1714C>T (p.Arg572Ter)

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.1714C>T (p.Arg572Ter)
HGVS:
  • NC_000002.12:g.188996449C>T
  • NG_007404.1:g.27077C>T
  • NM_000090.4:c.1714C>TMANE SELECT
  • NP_000081.1:p.Arg572Ter
  • NP_000081.2:p.Arg572Ter
  • LRG_3t1:c.1714C>T
  • LRG_3:g.27077C>T
  • LRG_3p1:p.Arg572Ter
  • NC_000002.11:g.189861175C>T
  • NM_000090.3:c.1714C>T
Protein change:
R572*
Molecular consequence:
  • NM_000090.4:c.1714C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Ehlers-Danlos syndrome (EDS)
Synonyms:
ED syndrome
Identifiers:
MONDO: MONDO:0020066; MedGen: C0013720; OMIM: PS130000

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004847863Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely Pathogenic
(Oct 11, 2019) 		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 Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV004847863.1

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

Description

Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: The p.Arg572X variant in COL3A1 has not been previously reported in individuals with Ehlers-Danlos syndrome (EDS) and was absent from large population studies. This nonsense variant leads to a premature termination codon at position 572, which is predicted to lead to a truncated or absent protein. Heterozygous loss of function of the COL3A1 gene is an established disease mechanism in Ehlers-Danlos syndrome and is associated with late-onset, reduced penetrance, and possibly a milder clinical course (Leistritz 2011, Frank 2015). In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant EDS. ACMG/AMP Criteria applied: PVS1, PM2.

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

Last Updated: May 1, 2024