ATP11B

protein-coding

ATPase phospholipid transporting 11B (putative), the group of ATPase phospholipid transporting

Gene summary

P-type ATPases, such as ATP11B, are phosphorylated in their intermediate state and drive uphill transport of ions across membranes. Several subfamilies of P-type ATPases have been identified. One subfamily transports heavy metal ions, such as Cu(2+) or Cd(2+). Another subfamily transports non-heavy metal ions, such as H(+), Na(+), K(+), or Ca(+). A third subfamily transports amphipaths, such as phosphatidylserine.[supplied by OMIM, Feb 2005]

MANE transcript

NM_014616.3

Inheritance

—

ClinVar variants

U:128B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr3:182,793,503-182,923,011

External References & Databases

Ensembl (ENSG00000058063)

Transcript & Mutation Effects

hg38 • Region Span ~129.5 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 ATP11B variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 120

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014616.3. 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
missense			122 clinvar	2 clinvar		124
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	128	2	0	130

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014616.3	RefSeq	NP_055431.1	30	MANE Select
ENST00000323116.10	Ensembl	ENSP00000321195.5	30	MANE Select
ENST00000466758.5	Ensembl	ENSP00000417406.1	4	Standard
ENST00000475636.2	Ensembl	ENSP00000520748.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neutrophil degranulation
Ion channel transport
Purine metabolism
Innate Immune System
Immune System

Biological Process

ion transport
aminophospholipid transport
ion transmembrane transport
neutrophil degranulation
phospholipid translocation

Molecular Function

magnesium ion binding
phospholipid-translocating ATPase activity
protein binding
ATP binding
ion transmembrane transporter activity

Cellular Component

nuclear inner membrane
early endosome
endoplasmic reticulum
trans-Golgi network
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000323116
Coding exons: 30
Length: 128136
Individuals with no LoFs: 125693
Homozygous LoFs: 0
Heterozygous LoFs: 55
Defined: 125748
p: 0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.85	477	605	0.789	0.0000297	7718
Missense (PolyPhen)		115	227.54	0.50541		3014
Synonymous	0.982	191	209	0.914	0.0000106	2191
Loss of Function	5.56	19	68.7	0.276	0.00000363	849

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00039	0.00037	rare
Latino/Admixed American	0.00031	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00035	0.00033	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00022	0.00022	rare
South Asian	0.00017	0.00016	rare
Other	0	0.0	absent

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). Involved in regulation of sensitivity to cisplatin; may contribute to secretory vesicle transport of cisplatin from Golgi to plasma membrane. {ECO:0000269|PubMed:23585472, ECO:0000305}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.429
RVIS EVS: -0.44
RVIS percentile EVS: 24.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.341

Gene Damage Prediction

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