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NM_000090.4(COL3A1):c.1189G>T (p.Glu397Ter) AND Ehlers-Danlos syndrome, type 4

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 6, 2019
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001253763.2

Allele description [Variation Report for NM_000090.4(COL3A1):c.1189G>T (p.Glu397Ter)]

NM_000090.4(COL3A1):c.1189G>T (p.Glu397Ter)

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.1189G>T (p.Glu397Ter)
HGVS:
  • NC_000002.12:g.188994077G>T
  • NG_007404.1:g.24705G>T
  • NM_000090.4:c.1189G>TMANE SELECT
  • NP_000081.2:p.Glu397Ter
  • LRG_3t1:c.1189G>T
  • LRG_3:g.24705G>T
  • NC_000002.11:g.189858803G>T
  • NM_000090.3:c.1189G>T
  • p.Glu397*
Protein change:
E397*
Links:
dbSNP: rs187907868
NCBI 1000 Genomes Browser:
rs187907868
Molecular consequence:
  • NM_000090.4:c.1189G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Ehlers-Danlos syndrome, type 4
Synonyms:
Ehlers-Danlos syndrome vascular type; Ehlers Danlos syndrome, ecchymotic type; Ehlers Danlos syndrome, arterial type; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0017314; MedGen: C0268338; Orphanet: 286; OMIM: 130050

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001427067Clinical Genomics Laboratory, Stanford Medicine
no assertion criteria provided
Likely pathogenic
(Aug 6, 2019) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From Clinical Genomics Laboratory, Stanford Medicine, SCV001427067.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testingnot provided

Description

The p.Glu397* variant in the COL3A1 gene has not been previously reported in association with disease. This variant was absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). The p.Glu397* variant leads to a premature stop codon in exon 17 of 51 coding exons, and is therefore predicted to undergo nonsense-mediated decay resulting in a truncated or absent protein. Heterozygous loss of function is an established mechanism of disease for the COL3A1 gene. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the p.Glu397* variant as likely pathogenic for vascular Ehlers-Danlos syndrome in an autosomal dominant manner based on the information above. [ACMG evidence codes used: PVS1; PM2]

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

Last Updated: Jul 7, 2024