NM_000443.4(ABCB4):c.959C>T (p.Ser320Phe) AND ABCB4-related disorder

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 28, 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:: RCV004532350.1

Allele description [Variation Report for NM_000443.4(ABCB4):c.959C>T (p.Ser320Phe)]

NM_000443.4(ABCB4):c.959C>T (p.Ser320Phe)

Gene:

ABCB4:ATP binding cassette subfamily B member 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q21.12

Genomic location:

Preferred name:

NM_000443.4(ABCB4):c.959C>T (p.Ser320Phe)

HGVS:

NC_000007.14:g.87447080G>A
NG_007118.2:g.38353C>T
NM_000443.4:c.959C>TMANE SELECT
NM_018849.3:c.959C>T
NM_018850.3:c.959C>T
NP_000434.1:p.Ser320Phe
NP_061337.1:p.Ser320Phe
NP_061338.1:p.Ser320Phe
NC_000007.13:g.87076396G>A
NM_000443.3:c.959C>T
NM_018849.2:c.959C>T
P21439:p.Ser320Phe

Protein change:

S320F; SER320PHE

Links:

UniProtKB: P21439#VAR_023502; OMIM: 171060.0005; dbSNP: rs72552778

NCBI 1000 Genomes Browser:

rs72552778

Molecular consequence:

NM_000443.4:c.959C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_018849.3:c.959C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_018850.3:c.959C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: ABCB4-related disorder
Synonyms:: ABCB4-related disorders; ABCB4-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004115331	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 28, 2023)	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

SCV004115331

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Nov 28, 2023)

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	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 PreventionGenetics, part of Exact Sciences, SCV004115331.2

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

Description

The ABCB4 c.959C>T variant is predicted to result in the amino acid substitution p.Ser320Phe. This variant has been reported in the homozygous or compound heterozygous state in several individuals with cholestasis phenotypes (see for example, Rosmorduc et al. 2001. PubMed ID: 11313316; Keitel et al. 2006. PubMed ID: 16890614; Degiorgio et al. 2007 PubMed ID: 17726488). In vitro functional assessment has been inconclusive (Kim et al. 2013. PubMed ID: 24381502; Andress et al. 2014. PubMed ID: 24806754; Gordo-Gilart et al. 2015. PubMed ID: 26153658). This variant is reported in 0.029% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as likely 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: Jul 15, 2024

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