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NM_001374385.1(ATP8B1):c.1982T>C (p.Ile661Thr) AND Benign recurrent intrahepatic cholestasis type 1

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Mar 24, 2024
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:
RCV000007689.10

Allele description [Variation Report for NM_001374385.1(ATP8B1):c.1982T>C (p.Ile661Thr)]

NM_001374385.1(ATP8B1):c.1982T>C (p.Ile661Thr)

Gene:
ATP8B1:ATPase phospholipid transporting 8B1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
18q21.31
Genomic location:
Preferred name:
NM_001374385.1(ATP8B1):c.1982T>C (p.Ile661Thr)
HGVS:
  • NC_000018.10:g.57669433A>G
  • NG_007148.3:g.139390T>C
  • NM_001374385.1:c.1982T>CMANE SELECT
  • NM_001374386.1:c.1832T>C
  • NM_005603.6:c.1982T>C
  • NP_001361314.1:p.Ile661Thr
  • NP_001361315.1:p.Ile611Thr
  • NP_005594.1:p.Ile661Thr
  • NP_005594.2:p.Ile661Thr
  • LRG_1205t1:c.1982T>C
  • LRG_1205:g.139390T>C
  • LRG_1205p1:p.Ile661Thr
  • NC_000018.9:g.55336665A>G
  • NM_005603.4:c.1982T>C
  • NM_005603.5:c.1982T>C
  • O43520:p.Ile661Thr
Protein change:
I611T; ILE661THR
Links:
UniProtKB: O43520#VAR_008812; OMIM: 602397.0006; dbSNP: rs121909100
NCBI 1000 Genomes Browser:
rs121909100
Molecular consequence:
  • NM_001374385.1:c.1982T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374386.1:c.1832T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005603.6:c.1982T>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Benign recurrent intrahepatic cholestasis type 1
Synonyms:
Summerskill syndrome; Recurrent familial intrahepatic cholestasis 1
Identifiers:
MONDO: MONDO:0009469; MedGen: C4551899; Orphanet: 65682; OMIM: 243300

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000027890OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 2004)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV002580065MGZ Medical Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 13, 2022)
germlineclinical testing

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

SCV004210707Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 24, 2024)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

A gene encoding a P-type ATPase mutated in two forms of hereditary cholestasis.

Bull LN, van Eijk MJ, Pawlikowska L, DeYoung JA, Juijn JA, Liao M, Klomp LW, Lomri N, Berger R, Scharschmidt BF, Knisely AS, Houwen RH, Freimer NB.

Nat Genet. 1998 Mar;18(3):219-24.

PubMed [citation]
PMID:
9500542

Recurrent familial intrahepatic cholestasis in the Faeroe Islands. Phenotypic heterogeneity but genetic homogeneity.

Tygstrup N, Steig BA, Juijn JA, Bull LN, Houwen RH.

Hepatology. 1999 Feb;29(2):506-8.

PubMed [citation]
PMID:
9918928
See all PubMed Citations (5)

Details of each submission

From OMIM, SCV000027890.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

In a patient with benign recurrent intrahepatic cholestasis-1 (BRIC1; 243300), Bull et al. (1998) identified a 1982T-C transition in the ATP8B1 gene, resulting in an ile661-to-thr (I661T) amino acid substitution. The nonconservative mutation was at a site at which all members of the subfamily of P-type ATPases to which ATP8B1 belongs have a leucine or isoleucine residue. The mutation was present on the most common conserved haplotype in BRIC patients of western European descent. It was present in homozygous form in patients from 13 families and in heterozygous form in patients from 6 additional families, and was not found on 84 control chromosomes.

Tygstrup et al. (1999) identified homozygosity for the I661T mutation in 5 males with BRIC from the Faroe Islands who were originally reported by Tygstrup and Jensen (1969). Haplotype analysis suggested a founder effect.

Klomp et al. (2004) identified the I661T mutation in 14 BRIC families; 3 families were homozygous, 8 were compound heterozygous with another ATP8B1 mutation, and in 3 families a second mutation was not identified. Two families with progressive familial intrahepatic cholestasis (PFIC; 211600) were compound heterozygous for the I661T mutation and another ATP8B1 mutation. In 1 family with BRIC, 4 individuals who were homozygous for the I661T mutation were symptom-free their entire lives, suggesting reduced penetrance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From MGZ Medical Genetics Center, SCV002580065.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Baylor Genetics, SCV004210707.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024