NM_000213.5(ITGB4):c.4012C>T (p.Gln1338Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 30, 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:: RCV003685816.2

Allele description [Variation Report for NM_000213.5(ITGB4):c.4012C>T (p.Gln1338Ter)]

NM_000213.5(ITGB4):c.4012C>T (p.Gln1338Ter)

Genes:

GALK1:galactokinase 1 [Gene - OMIM - HGNC]
ITGB4:integrin subunit beta 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q25.1

Genomic location:

Preferred name:

NM_000213.5(ITGB4):c.4012C>T (p.Gln1338Ter)

HGVS:

NC_000017.11:g.75752481C>T
NG_007372.1:g.36047C>T
NG_007372.2:g.36024C>T
NG_008079.2:g.17719G>A
NM_000213.5:c.4012C>TMANE SELECT
NM_001005619.1:c.4012C>T
NM_001005731.3:c.4012C>T
NM_001321123.2:c.4012C>T
NM_001381985.1:c.*23-744G>A
NP_000204.3:p.Gln1338Ter
NP_001005619.1:p.Gln1338Ter
NP_001005731.1:p.Gln1338Ter
NP_001308052.1:p.Gln1338Ter
LRG_1430:g.17719G>A
NC_000017.10:g.73748562C>T

Protein change:

Q1338*

Molecular consequence:

NM_001381985.1:c.*23-744G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000213.5:c.4012C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001005619.1:c.4012C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001005731.3:c.4012C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001321123.2:c.4012C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004413994	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 30, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 11328943, 16473856, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004413994

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 30, 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

Epidermolysis bullosa with congenital pyloric atresia: novel mutations in the beta 4 integrin gene (ITGB4) and genotype/phenotype correlations.

Nakano A, Pulkkinen L, Murrell D, Rico J, Lucky AW, Garzon M, Stevens CA, Robertson S, Pfendner E, Uitto J.

Pediatr Res. 2001 May;49(5):618-26.

PubMed [citation]

PMID:: 11328943

Epidermolysis bullosa. I. Molecular genetics of the junctional and hemidesmosomal variants.

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

J Med Genet. 2006 Aug;43(8):641-52. Epub 2006 Feb 10.

PubMed [citation]

PMID:: 16473856
PMCID:: PMC2564586

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004413994.1

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

Description

This sequence change creates a premature translational stop signal (p.Gln1338*) in the ITGB4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ITGB4 are known to be pathogenic (PMID: 11328943, 16473856). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ITGB4-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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: Nov 10, 2024

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