NM_000094.4(COL7A1):c.3727C>T (p.Arg1243Trp) AND not provided

Clinical significance:Uncertain significance

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001356939.1

Allele description [Variation Report for NM_000094.4(COL7A1):c.3727C>T (p.Arg1243Trp)]

NM_000094.4(COL7A1):c.3727C>T (p.Arg1243Trp)

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.3727C>T (p.Arg1243Trp)
HGVS:
  • NC_000003.12:g.48585972G>A
  • NG_007065.1:g.14281C>T
  • NM_000094.4:c.3727C>TMANE SELECT
  • NP_000085.1:p.Arg1243Trp
  • LRG_286:g.14281C>T
  • NC_000003.11:g.48623405G>A
Protein change:
R1243W
Molecular consequence:
  • NM_000094.4:c.3727C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001552240Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedUncertain significanceunknownclinical testing

Summary from all submissions

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

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001552240.1

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

Description

The COL7A1 p.R1243W variant was not identified in the literature nor was it identified in ClinVar. The variant was identified in dbSNP (ID: rs1189017197) and in control databases in 3 of 251292 chromosomes at a frequency of 0.00001194 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: South Asian in 2 of 30616 chromosomes (freq: 0.000065) and Latino in 1 of 34588 chromosomes (freq: 0.000029), but was not observed in the African, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), or Other populations. The p.R1243 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, MutationTaster, Revel, FATHMM, MetaLR, DANN) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (Splice AI exome) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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

Last Updated: Apr 12, 2021

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