NM_000094.4(COL7A1):c.5499C>T AND not provided

Clinical significance:Pathogenic (Last evaluated: Oct 24, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000414006.2

Allele description [Variation Report for NM_000094.4(COL7A1):c.5499C>T]

NM_000094.4(COL7A1):c.5499C>T

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_000094.4(COL7A1):c.5499C>T
HGVS:
  • NC_000003.12:g.48578354G>A
  • NG_007065.1:g.21899C>T
  • NM_000094.3:c.5499C>T
  • NM_000094.4:c.5499C>TMANE SELECT
  • NP_000085.1:p.Gly1833=
  • LRG_286t1:c.5499C>T
  • LRG_286:g.21899C>T
  • LRG_286p1:p.Gly1833=
  • NC_000003.11:g.48615787G>A
  • p.Glu1834Argfs*25
Links:
dbSNP: rs758886532
NCBI 1000 Genomes Browser:
rs758886532
Molecular consequence:
  • NM_000094.3:c.5499C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000490493GeneDxcriteria provided, single submitter
Pathogenic
(Oct 24, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000490493.2

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

Description

The c.5499 C>T; p.Gly1833Gly pathogenic variant in the COL7A1 gene has been reported previously as a pathogenic variant (Kern et al. 2009) and functional studies have shown that it creates a cryptic splice donor site in exon 64 resulting in the deletion of 35 bases and a frameshift resulting in a stop codon 25 amino acids upstream, denoted p.E1834RfsX25. The c.5499 C>T; p.Gly1833Gly variant was not observed in significant numbers within 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. In silico analysis predicts this variant probably results in the formation of a cryptic splice donor site in exon 64. Numerous other splicing variants in nearby residues have been reported in the Human Gene Mutation Database in association with DEB (Stenson et al., 2014), supporting the functional importance of this region of the protein. We interpret c.5499 C>T; p.Gly1833Gly as a pathogenic variant.

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

Last Updated: Apr 12, 2021

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