ATP10B

ATPase phospholipid transporting 10B (putative), the group of ATPase phospholipid transporting

Basic information

Region (hg38): 5:160563119-160852214

Links

ENSG00000118322 ∙ NCBI:23120 ∙ OMIM:619791 ∙ HGNC:13543 ∙ Uniprot:O94823 ∙ 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 ATP10B gene.

• Inborn genetic diseases (69 variants)
• not provided (9 variants)
• ATP10B-associated developmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP10B 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				1		1
missense			66	7	3	76
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	67	8	3

Variants in ATP10B

This is a list of pathogenic ClinVar variants found in the ATP10B region.

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

Position	Type	Phenotype	Significance	ClinVar
5-160565482-G-A		not specified	Uncertain significance (Jan 23, 2024)
5-160565493-C-T		not specified	Uncertain significance (May 23, 2023)
5-160565518-T-C		not specified	Uncertain significance (Dec 14, 2022)
5-160565521-G-C		not specified	Uncertain significance (Dec 28, 2022)
5-160565589-G-A		not specified	Uncertain significance (Jan 09, 2023)
5-160565595-C-A		not specified	Uncertain significance (Aug 13, 2021)
5-160565617-T-A		not specified	Uncertain significance (Nov 09, 2021)
5-160565836-C-A		not specified	Uncertain significance (Nov 09, 2022)
5-160565860-G-C		not specified	Uncertain significance (Aug 01, 2022)
5-160565864-C-A		not specified	Uncertain significance (Apr 11, 2023)
5-160565868-C-T		not specified	Uncertain significance (Jun 16, 2022)
5-160565879-T-A		not specified	Uncertain significance (Jun 21, 2022)
5-160569533-C-T		not specified	Uncertain significance (Aug 29, 2022)
5-160569559-T-C		not specified	Uncertain significance (Dec 18, 2023)
5-160569591-G-T		not specified	Uncertain significance (Jan 23, 2024)
5-160569643-A-G		not specified	Uncertain significance (Mar 07, 2024)
5-160569656-C-T		not specified	Uncertain significance (Jan 10, 2022)
5-160589597-T-C		not specified	Uncertain significance (Jun 14, 2023)
5-160589677-A-G			Benign (Jan 01, 2024)
5-160591127-A-G		not specified	Uncertain significance (May 09, 2023)
5-160591142-G-A			Uncertain significance (Mar 01, 2019)
5-160598829-T-A		not specified	Uncertain significance (Jul 25, 2023)
5-160598840-A-G		not specified	Uncertain significance (Jan 08, 2024)
5-160602579-C-T		not specified	Uncertain significance (Oct 10, 2023)
5-160602671-C-T		not specified	Uncertain significance (Feb 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP10B	protein_coding	protein_coding	ENST00000327245	22	289095

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.41e-30	0.00625	123384	17	1432	124833	0.00582

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0886	832	825	1.01	0.0000462	9586
Missense in Polyphen		263	320.93	0.8195		3827
Synonymous	-0.121	326	323	1.01	0.0000185	2857
Loss of Function	1.38	53	65.0	0.815	0.00000340	732

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00196	0.00194
Ashkenazi Jewish	0.000796	0.000695
East Asian	0.000838	0.000779
Finnish	0.0348	0.0337
European (Non-Finnish)	0.00566	0.00538
Middle Eastern	0.000838	0.000779
South Asian	0.00144	0.00134
Other	0.00325	0.00297

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). {ECO:0000305}.
• Pathway: Ion channel transport;Transport of small molecules;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.0998

Intolerance Scores

• loftool: 0.322
• rvis_EVS: 1.38
• rvis_percentile_EVS: 94.52

Haploinsufficiency Scores

• pHI: 0.143
• hipred: N
• hipred_score: 0.251
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.194

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp10b

Gene ontology

• Biological process: phospholipid translocation
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;integral component of membrane;cytoplasmic vesicle membrane
• Molecular function: magnesium ion binding;phospholipid-translocating ATPase activity;protein binding;ATP binding