ATP8B3
Basic information
Region (hg38): 19:1782075-1812276
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 11 | |||||
missense | 118 | 126 | ||||
nonsense | 3 | |||||
start loss | 0 | |||||
frameshift | 2 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 1 | 1 | 2 | |||
non coding | 2 | |||||
Total | 0 | 1 | 120 | 19 | 6 |
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) | ||
19-1783092-A-G | not specified | Uncertain significance (May 08, 2024) | ||
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) | ||
19-1784856-C-T | not specified | Uncertain significance (Mar 28, 2024) | ||
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) | ||
19-1785167-G-A | not specified | Uncertain significance (Apr 15, 2024) | ||
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) |
GnomAD
Source:
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:
- 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