ATP8B1
protein-codingATPase 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]
- FIC1
- BRIC
- PFIC1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~156.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0015762
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0008892
Submitter: Labcorp Genetics (formerly Invitae)
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.
Inheritance Pattern: AR
Disease ID:MONDO:0008892
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0007829
Submitter: PanelApp Australia
Inheritance Pattern: Unknown
Disease ID:MONDO:0007829
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0008892
Submitter: Orphanet
Clinical Genomic Database (CGD)
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ATP8B1 variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 8 | 345 | 5 | 360 | |
| missense | 3 | 29 | 369 | 23 | 5 | 429 |
| nonsense | 30 | 17 | 47 | |||
| start loss | 0 | |||||
| frameshift | 46 | 23 | 3 | 72 | ||
| splice donor/acceptor (+/-2bp) | 13 | 25 | 6 | 44 | ||
| Total | 92 | 96 | 386 | 368 | 10 | 952 |
Highest pathogenic variant AF is 0.0001592791
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001361314.1 | 27 | MANE Select | |
| Ensembl | ENSP00000497896.1 | 27 | MANE Select | |
| RefSeq | NP_001361315.1 | 26 | Standard | |
| RefSeq | NP_005594.2 | 27 | Standard |
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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.49 | 515 | 701 | 0.735 | 0.0000412 | 8262 |
| Missense (PolyPhen) | 169 | 283.67 | 0.59576 | 3412 | ||
| Synonymous | -0.230 | 273 | 268 | 1.02 | 0.0000174 | 2342 |
| Loss of Function | 4.59 | 29 | 70.6 | 0.411 | 0.00000391 | 789 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00061 | 0.00043 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00039 | 0.00039 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0.00065 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |