ATP8B2

protein-coding

ATPase phospholipid transporting 8B2, the group of ATPase phospholipid transporting

Gene summary

The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of aminophospholipid-transporting ATPases. The aminophospholipid translocases transport phosphatidylserine and phosphatidylethanolamine from one side of a bilayer to another. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001370597.1

Inheritance

—

ClinVar variants

U:106B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr1:154,325,525-154,351,304

External References & Databases

Ensembl (ENSG00000143515)

Transcript & Mutation Effects

hg38 • Region Span ~25.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATP8B2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 90

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001370597.1. 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 clinvar	2 clinvar	2 clinvar	6
missense			95 clinvar			95
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	106	2	2	110

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001370597.1	RefSeq	NP_001357526.1	27	MANE Select
ENST00000368489.6	Ensembl	ENSP00000357475.4	27	MANE Select
NM_001005855.2	RefSeq	NP_001005855.1	11	Standard
NM_001367934.1	RefSeq	NP_001354863.1	27	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Mesodermal Commitment Pathway
Ion channel transport
Transport of small molecules
Phosphatidylinositol phosphate metabolism
Glycerophospholipid metabolism

Biological Process

Golgi organization
ion transmembrane transport
phospholipid translocation

Molecular Function

magnesium ion binding
phospholipid-translocating ATPase activity
ATP binding

Cellular Component

endoplasmic reticulum membrane
Golgi apparatus
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368489
Coding exons: 28
Length: 25755
Individuals with no LoFs: 125705
Homozygous LoFs: 0
Heterozygous LoFs: 43
Defined: 125748
p: 0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.87	512	730	0.701	0.0000440	8079
Missense (PolyPhen)		228	346.09	0.65878		3853
Synonymous	1.09	267	291	0.919	0.0000176	2382
Loss of Function	5.35	17	62.7	0.271	0.00000320	688

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.00013	0.00013	rare
Other	0.00033	0.00033	rare

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 (Probable). {ECO:0000305}.;

Intolerance Scores

LoFtool: 0.0967
RVIS EVS: -1.66
RVIS percentile EVS: 2.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.384

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium