ATP8B3

ATPase phospholipid transporting 8B3, the group of ATPase phospholipid transporting

Basic information

Region (hg38): 19:1782074-1812276

Links

ENSG00000130270 ∙ NCBI:148229 ∙ OMIM:605866 ∙ HGNC:13535 ∙ Uniprot:O60423 ∙ 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 ATP8B3 gene.

• Inborn genetic diseases (90 variants)
• not provided (23 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP8B3 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				7	4	11
missense			85	7		92
nonsense		1	1		1	3
start loss						0
frameshift				2		2
inframe indel				1		1
splice donor/acceptor (+/-2bp)				1		1
splice region				1	1	2
non coding					1	1
Total	0	1	86	18	6

Highest pathogenic variant AF is 0.0000268

Variants in ATP8B3

This is a list of pathogenic ClinVar variants found in the ATP8B3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-1783078-G-A			Benign (Dec 31, 2019)
19-1783086-G-C		not specified	Uncertain significance (Apr 05, 2023)
19-1783126-T-C		not specified	Uncertain significance (Apr 25, 2023)
19-1783144-G-C		not specified	Uncertain significance (Dec 17, 2021)
19-1783171-A-G		not specified	Uncertain significance (Jan 10, 2023)
19-1783180-T-C		not specified	Uncertain significance (Jul 13, 2022)
19-1783197-G-C		not specified	Uncertain significance (Jul 12, 2022)
19-1783237-TCTC-T			Likely benign (Mar 29, 2018)
19-1783243-C-T		not specified	Uncertain significance (Sep 16, 2021)
19-1784836-T-G		not specified	Uncertain significance (May 09, 2023)
19-1784848-A-G		not specified	Uncertain significance (Nov 28, 2023)
19-1784914-T-C		not specified	Uncertain significance (Jan 08, 2024)
19-1784920-G-A		not specified	Uncertain significance (Sep 26, 2023)
19-1784944-C-T		not specified	Uncertain significance (Apr 28, 2022)
19-1785185-A-G		not specified	Uncertain significance (Jan 03, 2022)
19-1785215-G-A		not specified	Uncertain significance (Mar 11, 2024)
19-1785255-T-A		not specified	Likely benign (May 23, 2023)
19-1785257-G-A		not specified	Likely benign (Feb 16, 2023)
19-1785473-A-G		not specified	Uncertain significance (Feb 23, 2023)
19-1785474-T-C		not specified	Uncertain significance (Sep 06, 2022)
19-1785483-A-G		not specified	Uncertain significance (Jan 16, 2024)
19-1785540-C-T		not specified	Uncertain significance (Apr 07, 2022)
19-1785557-C-T		not specified	Uncertain significance (Jun 09, 2022)
19-1785576-T-G		not specified	Uncertain significance (Dec 02, 2022)
19-1785591-G-C		not specified	Uncertain significance (Dec 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP8B3	protein_coding	protein_coding	ENST00000310127	28	30202

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.47e-26	0.0283	124091	4	824	124919	0.00332

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.300	813	789	1.03	0.0000474	8417
Missense in Polyphen		267	282.18	0.94622		2945
Synonymous	-1.38	366	334	1.10	0.0000216	2529
Loss of Function	1.48	47	59.3	0.793	0.00000271	681

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00389	0.00374
Ashkenazi Jewish	0.0161	0.0158
East Asian	0.0110	0.0101
Finnish	0.000279	0.000278
European (Non-Finnish)	0.00273	0.00267
Middle Eastern	0.0110	0.0101
South Asian	0.00323	0.00308
Other	0.00237	0.00230

dbNSFP

Source: dbNSFP

• Function: FUNCTION: P4-ATPase flippase 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. May be responsible for the maintenance of asymmetric distribution of phosphatidylserine (PS) in spermatozoa membranes. Involved in acrosome reactions and binding of spermatozoa to zona pellucida. {ECO:0000250|UniProtKB:Q6UQ17}.
• Pathway: Ion channel transport;Transport of small molecules;Phosphatidylinositol phosphate metabolism;Glycerophospholipid metabolism;Vitamin A (retinol) metabolism;Ion transport by P-type ATPases (Consensus)

Intolerance Scores

• loftool: 0.391
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.22

Haploinsufficiency Scores

• pHI: 0.0766
• hipred: N
• hipred_score: 0.180
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.149

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp8b3
• Phenotype: cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: Golgi organization;binding of sperm to zona pellucida;phospholipid translocation
• Cellular component: acrosomal membrane;endoplasmic reticulum membrane;Golgi apparatus;plasma membrane;integral component of membrane
• Molecular function: magnesium ion binding;phospholipid-translocating ATPase activity;ATP binding