ATP10D

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

Basic information

Region (hg38): 4:47485275-47593486

Links

ENSG00000145246 ∙ NCBI:57205 ∙ OMIM:619815 ∙ HGNC:13549 ∙ Uniprot:Q9P241 ∙ 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 ATP10D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP10D 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			67	5	1	73
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	67	6	1

Variants in ATP10D

This is a list of pathogenic ClinVar variants found in the ATP10D region.

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

Position	Type	Phenotype	Significance	ClinVar
4-47512617-G-A		not specified	Uncertain significance (Jan 27, 2022)
4-47512620-C-G		not specified	Uncertain significance (Sep 21, 2023)
4-47512629-A-G		not specified	Uncertain significance (Oct 12, 2022)
4-47512635-C-T		not specified	Uncertain significance (Nov 15, 2021)
4-47512825-T-A		not specified	Uncertain significance (Jan 04, 2022)
4-47515514-A-G		not specified	Uncertain significance (Apr 13, 2022)
4-47515595-A-C		not specified	Uncertain significance (Dec 28, 2023)
4-47515616-G-A		not specified	Uncertain significance (Dec 27, 2023)
4-47515624-A-G		not specified	Uncertain significance (Jul 12, 2023)
4-47515664-A-G		not specified	Uncertain significance (Jan 04, 2022)
4-47522992-T-TA			Likely benign (Sep 07, 2023)
4-47523071-G-A			Benign (Sep 17, 2017)
4-47523085-G-A		not specified	Uncertain significance (Oct 27, 2021)
4-47523186-G-C		not specified	Uncertain significance (Jul 12, 2022)
4-47525587-A-G		not specified	Uncertain significance (Mar 15, 2024)
4-47525633-G-A		not specified	Uncertain significance (Feb 22, 2023)
4-47535529-G-A		not specified	Uncertain significance (Apr 25, 2022)
4-47535531-G-A		not specified	Uncertain significance (Dec 21, 2022)
4-47535904-C-T		not specified	Uncertain significance (May 24, 2024)
4-47535950-G-A		not specified	Uncertain significance (Dec 13, 2021)
4-47535997-A-G		not specified	Uncertain significance (Apr 20, 2024)
4-47536449-G-T		not specified	Uncertain significance (May 17, 2023)
4-47536456-C-A		not specified	Uncertain significance (Aug 02, 2023)
4-47536467-A-G		not specified	Uncertain significance (Oct 06, 2021)
4-47536708-A-C		not specified	Uncertain significance (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP10D	protein_coding	protein_coding	ENST00000273859	22	108199

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.56e-20	0.996	125483	0	265	125748	0.00105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.662	714	766	0.933	0.0000392	9341
Missense in Polyphen		244	308.83	0.79007		3812
Synonymous	-0.194	288	284	1.01	0.0000149	2775
Loss of Function	3.01	42	69.0	0.608	0.00000402	781

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000888	0.000887
Ashkenazi Jewish	0.00494	0.00487
East Asian	0.00169	0.00169
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000983	0.000967
Middle Eastern	0.00169	0.00169
South Asian	0.00139	0.00137
Other	0.000993	0.000978

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: 0.0945

Intolerance Scores

• loftool: 0.284
• rvis_EVS: 0.3
• rvis_percentile_EVS: 72.02

Haploinsufficiency Scores

• pHI: 0.0556
• hipred: N
• hipred_score: 0.377
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.230

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp10d

Gene ontology

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