ATP9B

protein-coding

ATPase phospholipid transporting 9B (putative), the group of ATPase phospholipid transporting

Gene summary

Predicted to enable ATPase-coupled intramembrane lipid carrier activity. Predicted to be involved in endocytosis; phospholipid translocation; and retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum. Located in perinuclear region of cytoplasm and trans-Golgi network. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_198531.5

Inheritance

—

ClinVar variants

U:194B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr18:79,069,285-79,378,287

External References & Databases

Ensembl (ENSG00000166377)

Transcript & Mutation Effects

hg38 • Region Span ~309.0 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 ATP9B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 175

not providedTotal: 13

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198531.5. 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	4 clinvar	3 clinvar	9
missense			185 clinvar	6 clinvar	1 clinvar	192
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	194	10	4	208

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 104 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198531.5	RefSeq	NP_940933.3	30	MANE Select
ENST00000426216.6	Ensembl	ENSP00000398076.2	30	MANE Select
NM_001306085.2	RefSeq	NP_001293014.1	29	Standard
ENST00000307671.12	Ensembl	ENSP00000304500.7	29	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ion channel transport
Transport of small molecules
Ion transport by P-type ATPases

Biological Process

retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
endocytosis
phospholipid translocation

Molecular Function

magnesium ion binding
phospholipid-translocating ATPase activity
ATP binding

Cellular Component

endosome
trans-Golgi network
plasma membrane
integral component of membrane
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000426216
Coding exons: 30
Length: 308999
Individuals with no LoFs: 125635
Homozygous LoFs: 0
Heterozygous LoFs: 113
Defined: 125748
p: 0.000449

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.691	634	685	0.926	0.0000417	7469
Missense (PolyPhen)		187	216.54	0.86359		2223
Synonymous	-0.363	281	273	1.03	0.0000185	2209
Loss of Function	3.63	34	65.7	0.517	0.00000331	746

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0013	0.0012	notable
Latino/Admixed American	0.00053	0.00052	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00050	0.00049	rare
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.00042	0.00042	rare
South Asian	0.00024	0.00023	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.227
RVIS EVS: -1.14
RVIS percentile EVS: 6.4

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.414

Gene Damage Prediction

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