ATP8B4

ATPase phospholipid transporting 8B4 (putative), the group of ATPase phospholipid transporting

Basic information

Region (hg38): 15:49858237-50182817

Links

ENSG00000104043 ∙ NCBI:79895 ∙ OMIM:609123 ∙ HGNC:13536 ∙ Uniprot:Q8TF62 ∙ 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 ATP8B4 gene.

• Inborn genetic diseases (44 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP8B4 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				2	1	3
missense			43	1	1	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	3	2

Variants in ATP8B4

This is a list of pathogenic ClinVar variants found in the ATP8B4 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-49860208-T-C		not specified	Uncertain significance (Jul 07, 2022)
15-49860211-T-C		not specified	Uncertain significance (Dec 09, 2023)
15-49860250-T-C		not specified	Uncertain significance (Apr 22, 2022)
15-49860252-C-T		not specified	Uncertain significance (Apr 06, 2022)
15-49860278-A-T			Benign (Apr 16, 2018)
15-49860325-C-T		not specified	Uncertain significance (Jul 26, 2023)
15-49860397-T-C		not specified	Uncertain significance (Dec 21, 2023)
15-49860411-C-T		not specified	Uncertain significance (Apr 13, 2022)
15-49860426-C-T		not specified	Uncertain significance (Jun 29, 2023)
15-49860472-G-A		not specified	Uncertain significance (Sep 26, 2023)
15-49862279-A-G		not specified	Uncertain significance (Nov 30, 2022)
15-49862318-G-A		not specified	Uncertain significance (Aug 17, 2022)
15-49862319-T-C		not specified	Uncertain significance (Dec 17, 2021)
15-49862357-A-G		not specified	Uncertain significance (Jan 23, 2024)
15-49866349-C-T		not specified	Uncertain significance (Feb 27, 2024)
15-49866439-T-G		not specified	Uncertain significance (Jan 26, 2022)
15-49866445-C-T		not specified	Uncertain significance (Oct 12, 2022)
15-49866463-A-G		not specified	Uncertain significance (Dec 14, 2022)
15-49876291-A-G		not specified	Uncertain significance (Sep 12, 2023)
15-49876342-A-G		not specified	Uncertain significance (Jan 26, 2022)
15-49876447-C-T		not specified	Uncertain significance (Dec 28, 2023)
15-49876448-G-T		not specified	Uncertain significance (Nov 08, 2022)
15-49876480-T-G		not specified	Uncertain significance (Mar 31, 2023)
15-49876495-C-A		not specified	Uncertain significance (Oct 28, 2023)
15-49876510-T-C		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP8B4	protein_coding	protein_coding	ENST00000284509	27	324580

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.67e-34	0.000346	125437	0	311	125748	0.00124

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.316	607	629	0.965	0.0000320	7878
Missense in Polyphen		222	253.62	0.87533		3175
Synonymous	0.476	214	223	0.959	0.0000113	2190
Loss of Function	0.919	56	63.9	0.876	0.00000331	780

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00199	0.00199
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.00431	0.00425
Finnish	0.000331	0.000323
European (Non-Finnish)	0.000977	0.000967
Middle Eastern	0.00431	0.00425
South Asian	0.00182	0.00180
Other	0.00135	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 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: Neutrophil degranulation;Ion channel transport;Innate Immune System;Immune System;Transport of small molecules;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.0851

Intolerance Scores

• loftool: 0.344
• rvis_EVS: 1.12
• rvis_percentile_EVS: 92.11

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.337
• ghis: 0.415

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp8b4

Gene ontology

• Biological process: Golgi organization;neutrophil degranulation;phospholipid translocation
• Cellular component: Golgi apparatus;plasma membrane;integral component of membrane;specific granule membrane;tertiary granule membrane
• Molecular function: magnesium ion binding;phospholipid-translocating ATPase activity;ATP binding