ATP8A1

ATPase phospholipid transporting 8A1, the group of ATPase phospholipid transporting

Basic information

Region (hg38): 4:42408373-42657121

Links

ENSG00000124406 ∙ NCBI:10396 ∙ OMIM:609542 ∙ HGNC:13531 ∙ Uniprot:Q9Y2Q0 ∙ 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 ATP8A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP8A1 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			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	34	1	0

Variants in ATP8A1

This is a list of pathogenic ClinVar variants found in the ATP8A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-42414656-C-T		not specified	Uncertain significance (Jul 10, 2024)
4-42422853-G-T		not specified	Uncertain significance (Dec 07, 2023)
4-42422903-C-A			Likely benign (Dec 31, 2019)
4-42423618-C-T		not specified	Uncertain significance (Jul 12, 2022)
4-42423648-C-T		not specified	Uncertain significance (Oct 29, 2021)
4-42443575-A-G		not specified	Uncertain significance (Oct 20, 2024)
4-42443630-C-G		not specified	Uncertain significance (Dec 27, 2023)
4-42452038-T-G		not specified	Uncertain significance (Sep 25, 2024)
4-42452043-C-G		not specified	Uncertain significance (May 27, 2022)
4-42455316-G-C		not specified	Uncertain significance (Oct 01, 2024)
4-42455599-T-C		not specified	Uncertain significance (Aug 27, 2024)
4-42464784-T-A		not specified	Uncertain significance (May 06, 2022)
4-42464898-C-T		not specified	Uncertain significance (Feb 10, 2022)
4-42465018-C-T		not specified	Likely benign (Feb 24, 2023)
4-42485560-T-C		not specified	Uncertain significance (Nov 15, 2024)
4-42485566-C-A		not specified	Uncertain significance (Oct 06, 2021)
4-42485635-T-C		not specified	Uncertain significance (Feb 02, 2023)
4-42485642-G-C		not specified	Uncertain significance (Jun 06, 2023)
4-42485643-T-C		not specified	Uncertain significance (Nov 09, 2023)
4-42485647-G-A		not specified	Uncertain significance (Aug 13, 2021)
4-42503502-T-C		not specified	Uncertain significance (Jan 23, 2024)
4-42507094-T-C		not specified	Uncertain significance (Jul 09, 2024)
4-42507108-T-C		not specified	Uncertain significance (Dec 14, 2023)
4-42522209-A-G		not specified	Uncertain significance (Jan 30, 2024)
4-42522246-C-T		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP8A1	protein_coding	protein_coding	ENST00000381668	37	248733

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.200	0.800	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.61	427	608	0.702	0.0000309	7607
Missense in Polyphen		180	292.3	0.6158		3823
Synonymous	-0.289	226	221	1.02	0.0000120	2170
Loss of Function	6.24	18	77.2	0.233	0.00000404	920

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000366	0.000365
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000276	0.000272
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000256	0.000255
Middle Eastern	0.000276	0.000272
South Asian	0.0000653	0.0000653
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. In vitro, its ATPase activity is selectively and stereospecifically stimulated by phosphatidylserine (PS). The flippase complex ATP8A1:TMEM30A seems to play a role in regulation of cell migration probably involving flippase-mediated translocation of phosphatidylethanolamine (PE) at the plasma membrane. Acts as aminophospholipid translocase at the plasma membrane in neuronal cells.
• Pathway: Peptide GPCRs;Neutrophil degranulation;Ion channel transport;Innate Immune System;Immune System;Transport of small molecules;Phosphatidylinositol phosphate metabolism;Glycerophospholipid metabolism;Vitamin A (retinol) metabolism;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.204
• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.68

Haploinsufficiency Scores

• pHI: 0.799
• hipred: Y
• hipred_score: 0.685
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.291

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp8a1
• Phenotype: hematopoietic system phenotype; growth/size/body region phenotype; normal phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: learning;positive regulation of cell migration;ion transmembrane transport;neutrophil degranulation;phospholipid translocation;positive regulation of phospholipid translocation;ATP hydrolysis coupled cation transmembrane transport
• Cellular component: endoplasmic reticulum;Golgi apparatus;trans-Golgi network;plasma membrane;membrane;integral component of membrane;azurophil granule membrane;specific granule membrane;chromaffin granule membrane;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: magnesium ion binding;phospholipid-translocating ATPase activity;protein binding;ATP binding;cation-transporting ATPase activity