NM_000094.4(COL7A1):c.5576_5577del (p.Lys1859fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 17, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003727987.2

Allele description [Variation Report for NM_000094.4(COL7A1):c.5576_5577del (p.Lys1859fs)]

NM_000094.4(COL7A1):c.5576_5577del (p.Lys1859fs)

Gene:

COL7A1:collagen type VII alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3p21.31

Genomic location:

Preferred name:

NM_000094.4(COL7A1):c.5576_5577del (p.Lys1859fs)

HGVS:

NC_000003.12:g.48576912_48576913del
NG_007065.1:g.23341_23342del
NM_000094.4:c.5576_5577delMANE SELECT
NP_000085.1:p.Lys1859fs
LRG_286:g.23341_23342del
NC_000003.11:g.48614344_48614345del
NC_000003.11:g.48614345_48614346del
NM_000094.4:c.5576_5577delAAMANE SELECT
p.Lys1859Argfs*12

Protein change:

K1859fs

Links:

dbSNP: rs2044349915

NCBI 1000 Genomes Browser:

rs2044349915

Molecular consequence:

NM_000094.4:c.5576_5577del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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sulfiredoxin-1 [Homo sapiens]
sulfiredoxin-1 [Homo sapiens]
gi|22129778|ref|NP_542763.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004535325	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 17, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 31001817, 16971478, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004535325

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 17, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

Epidermolysis bullosa. II. Type VII collagen mutations and phenotype-genotype correlations in the dystrophic subtypes.

Varki R, Sadowski S, Uitto J, Pfendner E.

J Med Genet. 2007 Mar;44(3):181-92. Epub 2006 Sep 13.

PubMed [citation]

PMID:: 16971478
PMCID:: PMC2598021

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004535325.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1047940). This premature translational stop signal has been observed in individual(s) with autosomal recessive epidermolysis bullosa dystrophica (PMID: 31001817). This sequence change creates a premature translational stop signal (p.Lys1859Argfs*12) in the COL7A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COL7A1 are known to be pathogenic (PMID: 16971478).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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