ClinVar Miner

Submissions for variant NM_000090.4(COL3A1):c.1786C>T (p.Arg596Ter)

dbSNP: rs587779527
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000497775 SCV000589615 pathogenic not provided 2022-11-20 criteria provided, single submitter clinical testing Identified in compound heterozygous state with a missense COL3A1 variant in two siblings with vEDS; however, family members who were only heterozygous for p.(R596*) had no major features of vEDS, indicating marked clinical variability (Pepin et al., 2014; Jorgensen et al., 2015); Not observed at significant frequency in large population cohorts (gnomAD); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 25205403, 28258187, 30474650, 24922459, 25758994)
Fulgent Genetics, Fulgent Genetics RCV000763468 SCV000894248 pathogenic Ehlers-Danlos syndrome, type 4 2018-10-31 criteria provided, single submitter clinical testing
SIB Swiss Institute of Bioinformatics RCV000758208 SCV000996419 pathogenic Polymicrogyria with or without vascular-type Ehlers-Danlos syndrome 2019-07-08 criteria provided, single submitter curation This variant is interpreted as a Pathogenic for Polymicrogyria with or without vascular-type Ehlers-Danlos syndrome, autosomal recessive. The following ACMG Tag(s) were applied: PM2, PVS1, PP1.
Labcorp Genetics (formerly Invitae), Labcorp RCV000763468 SCV001391962 pathogenic Ehlers-Danlos syndrome, type 4 2023-04-24 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 242648). This premature translational stop signal has been observed in individual(s) with Ehlers-Danlos syndrome, vascular type (PMID: 25205403, 25758994). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg596*) in the COL3A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COL3A1 are known to be pathogenic (PMID: 24922459).
OMIM RCV000758208 SCV000886728 pathogenic Polymicrogyria with or without vascular-type Ehlers-Danlos syndrome 2019-03-05 no assertion criteria provided literature only

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