ATP8B4

protein-coding

ATPase phospholipid transporting 8B4 (putative), the group of ATPase phospholipid transporting

Gene summary

This gene encodes a member of the cation transport ATPase (P-type) family and type IV subfamily. The encoded protein is involved in phospholipid transport in the cell membrane. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]

MANE transcript

NM_024837.4

Inheritance

—

ClinVar variants

U:166B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr15:49,858,238-50,182,817

External References & Databases

Ensembl (ENSG00000104043)

Transcript & Mutation Effects

hg38 • Region Span ~324.6 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 ATP8B4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 163

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024837.4. 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				3 clinvar	1 clinvar	4
missense			164 clinvar	5 clinvar	1 clinvar	170
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	166	8	2	176

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 78 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024837.4	RefSeq	NP_079113.2	27	MANE Select
ENST00000284509.11	Ensembl	ENSP00000284509.6	27	MANE Select
ENST00000557955.5	Ensembl	ENSP00000453690.1	20	Standard
ENST00000558024.1	Ensembl	ENSP00000453143.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neutrophil degranulation
Ion channel transport
Innate Immune System
Immune System
Transport of small molecules

Biological Process

Golgi organization
neutrophil degranulation
phospholipid translocation

Molecular Function

magnesium ion binding
phospholipid-translocating ATPase activity
ATP binding

Cellular Component

Golgi apparatus
plasma membrane
integral component of membrane
specific granule membrane
tertiary granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000284509
Coding exons: 27
Length: 324580
Individuals with no LoFs: 125437
Homozygous LoFs: 0
Heterozygous LoFs: 311
Defined: 125748
p: 0.00124

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.316	607	629	0.965	0.0000320	7878
Missense (PolyPhen)		222	253.62	0.87533		3175
Synonymous	0.476	214	223	0.959	0.0000113	2190
Loss of Function	0.919	56	63.9	0.876	0.00000331	780

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00086	0.00086	rare
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.0043	0.0042	notable
Finnish	0.00033	0.00032	rare
European (Non-Finnish)	0.00098	0.00097	rare
South Asian	0.0018	0.0018	notable
Other	0.0014	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: 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}.;

Recessive Scores

pRec: 0.0851

Intolerance Scores

LoFtool: 0.344
RVIS EVS: 1.12
RVIS percentile EVS: 92.11

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.291

Gene Damage Prediction

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