ATP11B

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

Basic information

Region (hg38): 3:182793503-182923011

Links

ENSG00000058063 ∙ NCBI:23200 ∙ OMIM:605869 ∙ HGNC:13553 ∙ Uniprot:Q9Y2G3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP11B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP11B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			64	2		66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	64	2	0

Variants in ATP11B

This is a list of pathogenic ClinVar variants found in the ATP11B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-182820277-T-G		not specified	Uncertain significance (Dec 07, 2023)
3-182820302-G-A		not specified	Likely benign (Nov 29, 2023)
3-182820329-C-T		not specified	Uncertain significance (Jan 26, 2023)
3-182820350-A-G		not specified	Uncertain significance (Apr 09, 2024)
3-182829744-A-G		not specified	Uncertain significance (Aug 13, 2021)
3-182836057-A-G		not specified	Uncertain significance (Jan 22, 2025)
3-182836071-G-A		not specified	Uncertain significance (Apr 14, 2022)
3-182836412-G-A		not specified	Uncertain significance (Aug 04, 2023)
3-182837092-A-G		not specified	Uncertain significance (Oct 22, 2024)
3-182837117-A-G		not specified	Uncertain significance (Jan 22, 2024)
3-182837140-A-G		not specified	Uncertain significance (Mar 17, 2023)
3-182842086-G-A		not specified	Uncertain significance (Jul 09, 2021)
3-182845468-C-T		not specified	Uncertain significance (Sep 20, 2023)
3-182848482-C-T		not specified	Uncertain significance (Mar 25, 2024)
3-182857952-A-G		not specified	Uncertain significance (May 29, 2024)
3-182858021-G-C		not specified	Uncertain significance (Sep 13, 2023)
3-182865561-C-G		not specified	Uncertain significance (Jan 03, 2022)
3-182865619-G-C		not specified	Uncertain significance (Sep 03, 2024)
3-182866289-T-G		not specified	Uncertain significance (Jun 18, 2021)
3-182866352-G-A		not specified	Uncertain significance (Mar 08, 2025)
3-182866376-G-A		not specified	Uncertain significance (May 16, 2024)
3-182867415-G-A		not specified	Uncertain significance (Jan 23, 2024)
3-182867432-G-C		not specified	Uncertain significance (Jan 07, 2022)
3-182867440-G-C		not specified	Uncertain significance (Jan 16, 2025)
3-182872383-T-C		not specified	Uncertain significance (Dec 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP11B	protein_coding	protein_coding	ENST00000323116	30	128136

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00201	0.998	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	477	605	0.789	0.0000297	7718
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000699	0.000675
Ashkenazi Jewish	0.00	0.00
East Asian	0.000345	0.000326
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000223	0.000220
Middle Eastern	0.000345	0.000326
South Asian	0.000167	0.000163
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Neutrophil degranulation;Ion channel transport;Purine metabolism;Innate Immune System;Immune System;Transport of small molecules;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.429
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.6

Haploinsufficiency Scores

• pHI: 0.230
• hipred: Y
• hipred_score: 0.528
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp11b

Gene ontology

• Biological process: ion transport;aminophospholipid transport;ion transmembrane transport;neutrophil degranulation;phospholipid translocation
• Cellular component: nuclear inner membrane;early endosome;endoplasmic reticulum;trans-Golgi network;plasma membrane;membrane;integral component of membrane;azurophil granule membrane;recycling endosome;recycling endosome membrane
• Molecular function: magnesium ion binding;phospholipid-translocating ATPase activity;protein binding;ATP binding;ion transmembrane transporter activity