ATP8B1

protein-coding

ATPase phospholipid transporting 8B1, the group of ATPase phospholipid transporting

Gene summary

This gene encodes a member of the P-type cation transport ATPase family, which belongs to the subfamily of aminophospholipid-transporting ATPases. The aminophospholipid translocases transport phosphatidylserine and phosphatidylethanolamine from one side of a bilayer to another. Mutations in this gene may result in progressive familial intrahepatic cholestasis type 1 and in benign recurrent intrahepatic cholestasis. [provided by RefSeq, Jul 2008]

Previous symbols:
  • FIC1
  • BRIC
  • PFIC1

MANE transcript

NM_001374385.1

Inheritance

AR, AD

ClinVar variants

P:188U:386B:378

Top phenotype

Familial intrahepatic cholestasis, recurrent; Cholestasis, progressive familial intrahepatic 1; Intrahepatic cholestasis of pregnancy

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr18:57,646,426-57,803,315

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~156.9 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

progressive familial intrahepatic cholestasisSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0015762

Submitter: PanelApp Australia

progressive familial intrahepatic cholestasis type 1STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008892

Submitter: Labcorp Genetics (formerly Invitae)

progressive familial intrahepatic cholestasis type 1DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008892

Submitter: Laboratory for Molecular Medicine

This gene-disease relationship has undergone rapid assessment. Classifications are based on preliminary review of gene-disease validity during analysis of genomic sequencing results.

progressive familial intrahepatic cholestasis type 1DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008892

Submitter: G2P

cholestasis, intrahepatic, of pregnancy, 1STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007829

Submitter: PanelApp Australia

cholestasis, intrahepatic, of pregnancy, 1LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0007829

Submitter: Labcorp Genetics (formerly Invitae)

progressive familial intrahepatic cholestasis type 1SUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008892

Submitter: Orphanet

Clinical Genomic Database (CGD)

Familial intrahepatic cholestasis, recurrent; Cholestasis, progressive familial intrahepatic 1; Intrahepatic cholestasis of pregnancyAD/AR

Manifestation: Gastrointestinal; Obstetric

Intervention: Gastrointestinal; Obstetric

Rationale: In severe forms, specific nutritional care may be beneficial (eg, including specific vitamin E supplementation); Hepatic manifestations may result in death in adolescence/early adulthood without surgical intervention; In pregnancy, Cholestasis, familial intrahepatic, of pregnancy, can cause severe sequelae (including death) in the fetus, as well as adverse maternal health outcomes, and precautions, including early delivery may be beneficial

Refs: 13840084; 5807632; 5762004; 5049818; 1218817; 3564958; 8088298; 7912266; 9500542; 9918928; 11093741; 15239083; 15448432; 15888793; 15657619; 20301474Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATP8B1 variants in ClinVar

13 Conditions Cataloged
not providedTotal: 746
Familial intrahepatic cholestasisTotal: 282
ATP8B1-related disorderTotal: 228
Progressive familial intrahepatic cholestasis type 1Total: 142
Inborn genetic diseasesTotal: 136
not specifiedTotal: 92
Benign recurrent intrahepatic cholestasis type 1Total: 83
Cholestasis, intrahepatic, of pregnancy, 1Total: 40

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001374385.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
8
clinvar
345
clinvar
5
clinvar
360
missense
3
clinvar
29
clinvar
369
clinvar
23
clinvar
5
clinvar
429
nonsense
30
clinvar
17
clinvar
47
start loss
0
frameshift
46
clinvar
23
clinvar
3
clinvar
72
splice donor/acceptor (+/-2bp)
13
clinvar
25
clinvar
6
clinvar
44
Total929638636810952

Highest pathogenic variant AF is 0.0001592791

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 52 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001374385.1RefSeqNP_001361314.127MANE Select
ENST00000648908.2EnsemblENSP00000497896.127MANE Select
NM_001374386.1RefSeqNP_001361315.126Standard
NM_005603.6RefSeqNP_005594.227Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Ion channel transport
  • Purine metabolism
  • Transport of small molecules
  • Phosphatidylinositol phosphate metabolism
  • Glycerophospholipid metabolism

Biological Process

  • drug transmembrane transport
  • Golgi organization
  • sensory perception of sound
  • bile acid and bile salt transport
  • regulation of microvillus assembly

Molecular Function

  • magnesium ion binding
  • phospholipid-translocating ATPase activity
  • protein binding
  • ATP binding

Cellular Component

  • endoplasmic reticulum
  • Golgi apparatus
  • plasma membrane
  • integral component of plasma membrane
  • apical plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000536015
Coding exons
27
Length
156676
Individuals with no LoFs
125664
Homozygous LoFs
0
Heterozygous LoFs
84
Defined
125748
p
0.000334
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.495157010.7350.00004128262
Missense (PolyPhen)169283.670.595763412
Synonymous-0.2302732681.020.00001742342
Loss of Function4.592970.60.4110.00000391789

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000250.00025rare
Latino/Admixed American0.000610.00043rare
Ashkenazi Jewish00.0absent
East Asian0.000380.00038rare
Finnish0.000140.00014rare
European (Non-Finnish)0.000390.00039rare
South Asian0.000230.00023rare
Other0.000650.00065rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Catalytic component of a P4-ATPase flippase complex which catalyzes the hydrolysis of ATP coupled to the transport of aminophospholipids from the outer to the inner leaflet of various membranes and ensures the maintenance of asymmetric distribution of phospholipids. Phospholipid translocation seems also to be implicated in vesicle formation and in uptake of lipid signaling molecules. May play a role in asymmetric distribution of phospholipids in the canicular membrane. May have a role in transport of bile acids into the canaliculus, uptake of bile acids from intestinal contents into intestinal mucosa or both. In cooperation with ABCB4 may be involved in establishing integrity of the canalicular membrane thus protecting hepatocytes from bile salts. Together with TMEM30A is involved in uptake of the synthetic drug alkylphospholipid perifosine. Involved in the microvillus formation in polarized epithelial cells; the function seems to be independent from its flippase activity. Required for the preservation of cochlear hair cells in the inner ear. May act as cardiolipin transporter during inflammatory injury. {ECO:0000269|PubMed:17948906, ECO:0000269|PubMed:20510206, ECO:0000269|PubMed:20512993}.;
Disease
DISEASE: Cholestasis, benign recurrent intrahepatic, 1 (BRIC1) [MIM:243300]: A disorder characterized by intermittent episodes of cholestasis without progression to liver failure. There is initial elevation of serum bile acids, followed by cholestatic jaundice which generally spontaneously resolves after periods of weeks to months. The cholestatic attacks vary in severity and duration. Patients are asymptomatic between episodes, both clinically and biochemically. {ECO:0000269|PubMed:15239083, ECO:0000269|PubMed:19731236, ECO:0000269|PubMed:9500542, ECO:0000269|PubMed:9918928}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cholestasis of pregnancy, intrahepatic 1 (ICP1) [MIM:147480]: A liver disorder of pregnancy. It presents during the second or, more commonly, the third trimester of pregnancy with intense pruritus which becomes more severe with advancing gestation and cholestasis. Cholestasis results from abnormal biliary transport from the liver into the small intestine. ICP1 causes fetal distress, spontaneous premature delivery and intrauterine death. ICP1 patients have spontaneous and progressive disappearance of cholestasis after delivery. {ECO:0000269|PubMed:15657619, ECO:0000269|PubMed:15888793, ECO:0000269|PubMed:19731236}. Note=The disease may be caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.167

Intolerance Scores

LoFtool
0.317
RVIS EVS
0.1
RVIS percentile EVS
60.76

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Indispensability pred.
N
Indispensability score
0.405

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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