NM_000094.3(COL7A1):c.7411C>T (p.Arg2471Ter) AND not provided

Clinical significance:Pathogenic (Last evaluated: May 25, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000255683.4

Allele description [Variation Report for NM_000094.3(COL7A1):c.7411C>T (p.Arg2471Ter)]

NM_000094.3(COL7A1):c.7411C>T (p.Arg2471Ter)

Gene:
COL7A1:collagen type VII alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.31
Genomic location:
Preferred name:
NM_000094.3(COL7A1):c.7411C>T (p.Arg2471Ter)
HGVS:
  • NC_000003.12:g.48570304G>A
  • NG_007065.1:g.29949C>T
  • NM_000094.3:c.7411C>T
  • NP_000085.1:p.Arg2471Ter
  • LRG_286t1:c.7411C>T
  • LRG_286:g.29949C>T
  • LRG_286p1:p.Arg2471Ter
  • NC_000003.11:g.48607737G>A
Protein change:
R2471*; ARG2471TER
Links:
OMIM: 120120.0037; dbSNP: rs121912852
NCBI 1000 Genomes Browser:
rs121912852
Molecular consequence:
  • NM_000094.3:c.7411C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000321511GeneDxcriteria provided, single submitter
Pathogenic
(Nov 15, 2019)
germlineclinical testing

Citation Link,

SCV001589400Invitaecriteria provided, single submitter
Pathogenic
(May 25, 2020)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Glycine substitutions in the triple-helical region of type VII collagen result in a spectrum of dystrophic epidermolysis bullosa phenotypes and patterns of inheritance.

Christiano AM, McGrath JA, Tan KC, Uitto J.

Am J Hum Genet. 1996 Apr;58(4):671-81.

PubMed [citation]
PMID:
8644729
PMCID:
PMC1914674

An overview of the genetic basis of epidermolysis bullosa in Brazil: discovery of novel and recurrent disease-causing variants.

Mariath LM, Santin JT, Frantz JA, Doriqui MJR, Kiszewski AE, Schuler-Faccini L.

Clin Genet. 2019 Sep;96(3):189-198. doi: 10.1111/cge.13555. Epub 2019 May 29. Review.

PubMed [citation]
PMID:
31001817
See all PubMed Citations (5)

Details of each submission

From GeneDx, SCV000321511.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 31001817, 25525159, 16271705, 18558993, 21448560, 8644729, 29473190)

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

From Invitae, SCV001589400.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Arg2471*) in the COL7A1 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs121912852, ExAC 0.001%). This variant has been observed in individual(s) with clinical features of autosomal recessive epidermolysis bullosa dystrophica (PMID: 8644729, 31001817,29473190). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 17459). Loss-of-function variants in COL7A1 are known to be pathogenic (PMID: 16971478). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 8, 2021

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