NM_003742.4(ABCB11):c.3556G>A (p.Glu1186Lys) AND Progressive familial intrahepatic cholestasis type 2

Germline classification:: Benign (2 submissions)
Last evaluated:: Apr 28, 2017
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:: RCV001133697.5

Allele description [Variation Report for NM_003742.4(ABCB11):c.3556G>A (p.Glu1186Lys)]

NM_003742.4(ABCB11):c.3556G>A (p.Glu1186Lys)

Gene:

ABCB11:ATP binding cassette subfamily B member 11 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q31.1

Genomic location:

Preferred name:

NM_003742.4(ABCB11):c.3556G>A (p.Glu1186Lys)

HGVS:

NC_000002.12:g.168927218C>T
NG_007374.2:g.109179G>A
NM_003742.4:c.3556G>AMANE SELECT
NP_003733.2:p.Glu1186Lys
LRG_1199t1:c.3556G>A
LRG_1199:g.109179G>A
LRG_1199p1:p.Glu1186Lys
NC_000002.11:g.169783728C>T
NG_007374.1:g.109106G>A
NM_003742.2:c.3556G>A
O95342:p.Glu1186Lys

Protein change:

E1186K

Links:

UniProtKB: O95342#VAR_030398; dbSNP: rs1521808

NCBI 1000 Genomes Browser:

rs1521808

Molecular consequence:

NM_003742.4:c.3556G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Progressive familial intrahepatic cholestasis type 2
Identifiers:: MONDO: MONDO:0011156; MedGen: C3489789; Orphanet: 79304; OMIM: 601847

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001293407	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Apr 28, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 20799350, 19101985, 20010382 Citation Link,
SCV001458318	Natera, Inc.	no assertion criteria provided	Benign (Jun 6, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001293407

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Apr 28, 2017)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV001458318

Natera, Inc.

no assertion criteria provided

Benign
(Jun 6, 2020)

germline

clinical testing

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

Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains.

Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A.

Protein Sci. 2010 Nov;19(11):2110-21. doi: 10.1002/pro.491.

PubMed [citation]

PMID:: 20799350
PMCID:: PMC3005782

Missense mutations and single nucleotide polymorphisms in ABCB11 impair bile salt export pump processing and function or disrupt pre-messenger RNA splicing.

Byrne JA, Strautnieks SS, Ihrke G, Pagani F, Knisely AS, Linton KJ, Mieli-Vergani G, Thompson RJ.

Hepatology. 2009 Feb;49(2):553-67. doi: 10.1002/hep.22683.

PubMed [citation]

PMID:: 19101985

See all PubMed Citations (3)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001293407.1

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

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. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.

#	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 Natera, Inc., SCV001458318.1

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 22, 2024

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