NM_000094.4(COL7A1):c.5820G>A (p.Pro1940=) AND Epidermolysis bullosa dystrophica

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Nov 26, 2018
Review status:: criteria provided, conflicting classifications

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:: RCV001148931.9

Allele description [Variation Report for NM_000094.4(COL7A1):c.5820G>A (p.Pro1940=)]

NM_000094.4(COL7A1):c.5820G>A (p.Pro1940=)

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.5820G>A (p.Pro1940=)

HGVS:

NC_000003.12:g.48576249C>T
NG_007065.1:g.24004G>A
NM_000094.4:c.5820G>AMANE SELECT
NP_000085.1:p.Pro1940=
NP_000085.1:p.Pro1940=
LRG_286t1:c.5820G>A
LRG_286:g.24004G>A
LRG_286p1:p.Pro1940=
NC_000003.11:g.48613682C>T
NM_000094.3:c.5820G>A
p.Gly1925_Pro1940del

Nucleotide change:

5820G-A

Links:

OMIM: 120120.0012; dbSNP: rs200972872

NCBI 1000 Genomes Browser:

rs200972872

Molecular consequence:

NM_000094.4:c.5820G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Epidermolysis bullosa dystrophica
Synonyms:: Dystrophic epidermolysis bullosa, Hallopeau-Siemens type (formerly); Dystrophic epidermolysis bullosa
Identifiers:: MONDO: MONDO:0006543; MedGen: C0079294

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001309852	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV001547333	Biomedical Innovation Departament, CIEMAT	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 26, 2018)	germline	research	PubMed (2) [See all records that cite these PMIDs] 9804332, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001309852

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Apr 27, 2017)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV001547333

Biomedical Innovation Departament, CIEMAT

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 26, 2018)

germline

research

PubMed (2)
[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	yes	4	not provided	not provided	not provided	not provided	research
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Compound heterozygosity for a recessive glycine substitution and a splice site mutation in the COL7A1 gene causes an unusually mild form of localized recessive dystrophic epidermolysis bullosa.

Terracina M, Posteraro P, Schubert M, Sonego G, Atzori F, Zambruno G, Bruckner-Tuderman L, Castiglia D.

J Invest Dermatol. 1998 Nov;111(5):744-50.

PubMed [citation]

PMID:: 9804332

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001309852.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

#	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

From Biomedical Innovation Departament, CIEMAT, SCV001547333.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	research	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		4	not provided	not provided	not provided

Last Updated: Apr 15, 2024

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