NM_000213.5(ITGB4):c.5336T>C (p.Leu1779Pro) AND Junctional epidermolysis bullosa with pyloric atresia

Germline classification:: Benign (3 submissions)
Last evaluated:: Aug 19, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000294224.8

Allele description [Variation Report for NM_000213.5(ITGB4):c.5336T>C (p.Leu1779Pro)]

NM_000213.5(ITGB4):c.5336T>C (p.Leu1779Pro)

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.5336T>C (p.Leu1779Pro)

HGVS:

NC_000017.11:g.75757422T>C
NG_007372.1:g.40988T>C
NG_008079.1:g.12778A>G
NM_000213.5:c.5336T>CMANE SELECT
NM_001005619.1:c.5285T>C
NM_001005731.3:c.5126T>C
NM_001321123.2:c.5126T>C
NP_000204.3:p.Leu1779Pro
NP_001005619.1:p.Leu1762Pro
NP_001005731.1:p.Leu1709Pro
NP_001308052.1:p.Leu1709Pro
NC_000017.10:g.73753503T>C
NM_000213.3:c.5336T>C
NM_001005731.1:c.5126T>C
P16144:p.Leu1779Pro

Protein change:

L1709P

Links:

UniProtKB: P16144#VAR_027804; dbSNP: rs871443

NCBI 1000 Genomes Browser:

rs871443

Molecular consequence:

NM_000213.5:c.5336T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001005619.1:c.5285T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001005731.3:c.5126T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001321123.2:c.5126T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Junctional epidermolysis bullosa with pyloric atresia
Synonyms:: EB-PA-ACC; Epidermolysis bullosa with pyloric atresia; Carmi syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009183; MedGen: C5676875; Orphanet: 79403; OMIM: 226730

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000406607	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification 20161018)	Benign (Jun 14, 2016)	germline	clinical testing	ICSL_Variant_Classification_20161018.pdf, Citation Link,
SCV001140833	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Benign (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV001980780	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Aug 19, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000406607

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification 20161018)

Benign
(Jun 14, 2016)

germline

clinical testing

ICSL_Variant_Classification_20161018.pdf,

Citation Link,

SCV001140833

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Benign
(May 28, 2019)

unknown

clinical testing

Citation Link,

SCV001980780

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Aug 19, 2021)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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, SCV000406607.2

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

#	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 Mendelics, SCV001140833.1

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

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

From Genome-Nilou Lab, SCV001980780.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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