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

Germline classification:
Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:
Jun 19, 2023
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:
RCV000007690.14

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]

Condition(s)

Name:
Progressive familial intrahepatic cholestasis type 1
Synonyms:
Byler's disease; Byler disease
Identifiers:
MONDO: MONDO:0008892; MedGen: C4551898; Orphanet: 79306; OMIM: 211600

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000147884GeneReviews
no classification provided
not providedgermlineliterature only

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

SCV000328232OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 2004)
germlineliterature only

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

SCV000914821Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)
Pathogenic
(Oct 16, 2018)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Citation Link,

SCV001140912Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2017)
Likely pathogenic
(Jun 19, 2023)
unknownclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, literature only
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Intermittent intrahepatic cholestasis of unknown etiology in five young males from the Faroe Islands.

Tygstrup N, Jensen B.

Acta Med Scand. 1969 Jun;185(6):523-30. No abstract available.

PubMed [citation]
PMID:
5807632

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
See all PubMed Citations (7)

Details of each submission

From GeneReviews, SCV000147884.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

At least 1 copy of this variant is found in most persons of European descent

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

From OMIM, SCV000328232.1

#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 Illumina Laboratory Services, Illumina, SCV000914821.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

Across a selection of available literature, the ATP8B1 c.1982T>C (p.Ile661Thr) variant has been reported in a homozygous state in 25 probands, in a compound heterozygous state in eight probands and in a heterozygous state in nine probands (Bull et al. 1998; Tygstrup et al. 1999; Klomp et al. 2004). The clinical presentation of many probands with this variant were described as having benign recurrent intrahepatic cholestatis, but some were described to have progressive disease. This disease has been noted to have reduced penetrance, and five individuals homozygous for the p.Ile661Thr variant were asymptomatic (Klomp et al. 2004). The p.Ile661Thr variant was absent from 289 controls and is reported at a frequency of 0.000158 in the European (non-Finnish) population of the Genome Aggregation Database. Functional studies to determine the effect of the p.Ile661Thr variant in cell lines document overall reduced protein expression compared to wild type (Folmer et al. 2009). Further investigation revealed the p.Ile661Thr variant to result in protein misfolding which was rescued by chemical chaperones such as 4-BPA (van der Velden et al. 2010; van der Woerd et al. 2016). Based on the collective evidence, the p.Ile661Thr variant is classified as pathogenic for familial intrahepatic cholestasis. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

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

From Mendelics, SCV001140912.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 24, 2024