NM_000443.4(ABCB4):c.879del (p.Ala294fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: May 31, 2022
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:: RCV000733982.7

Allele description [Variation Report for NM_000443.4(ABCB4):c.879del (p.Ala294fs)]

NM_000443.4(ABCB4):c.879del (p.Ala294fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

7q21.12

Genomic location:

Preferred name:

NM_000443.4(ABCB4):c.879del (p.Ala294fs)

HGVS:

NC_000007.14:g.87447165del
NG_007118.2:g.38273del
NM_000443.4:c.879delMANE SELECT
NM_018849.3:c.879del
NM_018850.3:c.879del
NP_000434.1:p.Ala294fs
NP_061337.1:p.Ala294fs
NP_061338.1:p.Ala294fs
NC_000007.13:g.87076476del
NC_000007.13:g.87076481del

Protein change:

A294fs

Links:

dbSNP: rs1326932143

NCBI 1000 Genomes Browser:

rs1326932143

Molecular consequence:

NM_000443.4:c.879del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_018849.3:c.879del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_018850.3:c.879del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

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
SCV000862090	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Pathogenic (Jun 20, 2018)	germline	clinical testing	Citation Link,
SCV003439980	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 31, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 23533021, 17726488, 25755532, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000862090

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL ClinVar v180209 classification definitions)

Pathogenic
(Jun 20, 2018)

germline

clinical testing

Citation Link,

SCV003439980

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 31, 2022)

germline

clinical testing

PubMed (4)
[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	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Genotype-phenotype relationships in the low-phospholipid-associated cholelithiasis syndrome: a study of 156 consecutive patients.

Poupon R, Rosmorduc O, Boëlle PY, Chrétien Y, Corpechot C, Chazouillères O, Housset C, Barbu V.

Hepatology. 2013 Sep;58(3):1105-10. doi: 10.1002/hep.26424. Epub 2013 Jul 29.

PubMed [citation]

PMID:: 23533021

Molecular characterization and structural implications of 25 new ABCB4 mutations in progressive familial intrahepatic cholestasis type 3 (PFIC3).

Degiorgio D, Colombo C, Seia M, Porcaro L, Costantino L, Zazzeron L, Bordo D, Coviello DA.

Eur J Hum Genet. 2007 Dec;15(12):1230-8. Epub 2007 Aug 29.

PubMed [citation]

PMID:: 17726488

See all PubMed Citations (4)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000862090.1

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003439980.2

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

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 597760). This premature translational stop signal has been observed in individual(s) with low phospholipid associated cholelithiasis (PMID: 23533021). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ala294Leufs*14) in the ABCB4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ABCB4 are known to be pathogenic (PMID: 17726488, 25755532).

#	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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