RPH3AL
rabphilin 3A like (without C2 domains)
Basic information
Region (hg38): 17:212388-386254
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (14 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPH3AL gene is commonly pathogenic or not.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 14 | 14 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice variant | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 14 | 0 | 0 |
Variants in RPH3AL
This is a list of pathogenic ClinVar variants found in the RPH3AL region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
17-213896-C-T | Inborn genetic diseases | Uncertain significance (Jun 11, 2021) | ||
17-215680-G-A | Inborn genetic diseases | Uncertain significance (Apr 25, 2022) | ||
17-215710-T-A | Inborn genetic diseases | Uncertain significance (Sep 07, 2022) | ||
17-215712-C-A | Inborn genetic diseases | Uncertain significance (Aug 10, 2021) | ||
17-215721-C-G | Inborn genetic diseases | Uncertain significance (Apr 07, 2023) | ||
17-215758-C-T | Inborn genetic diseases | Likely benign (Apr 11, 2023) | ||
17-215763-G-A | Inborn genetic diseases | Uncertain significance (Nov 08, 2022) | ||
17-215787-G-A | Inborn genetic diseases | Uncertain significance (Sep 16, 2021) | ||
17-219653-G-A | Inborn genetic diseases | Uncertain significance (Feb 07, 2023) | ||
17-219659-T-C | Inborn genetic diseases | Uncertain significance (Jun 29, 2023) | ||
17-219662-C-A | Inborn genetic diseases | Uncertain significance (Oct 03, 2022) | ||
17-219721-C-T | Inborn genetic diseases | Uncertain significance (Jul 22, 2022) | ||
17-247173-G-A | Inborn genetic diseases | Uncertain significance (Apr 07, 2022) | ||
17-247200-G-A | Inborn genetic diseases | Uncertain significance (Dec 28, 2022) | ||
17-247212-C-T | Inborn genetic diseases | Uncertain significance (Dec 13, 2022) | ||
17-247221-G-A | Inborn genetic diseases | Uncertain significance (Aug 10, 2021) | ||
17-247249-G-A | Inborn genetic diseases | Uncertain significance (Jan 24, 2023) | ||
17-247269-C-T | Inborn genetic diseases | Uncertain significance (Mar 06, 2023) | ||
17-247272-G-C | Inborn genetic diseases | Uncertain significance (Dec 20, 2021) | ||
17-251083-A-G | Inborn genetic diseases | Uncertain significance (May 09, 2023) | ||
17-252336-C-T | Inborn genetic diseases | Uncertain significance (Nov 01, 2022) | ||
17-252338-A-G | Inborn genetic diseases | Uncertain significance (Mar 01, 2023) | ||
17-252354-C-T | Inborn genetic diseases | Uncertain significance (Jun 28, 2022) | ||
17-327489-G-A | Inborn genetic diseases | Uncertain significance (Sep 13, 2023) | ||
17-327519-C-T | Inborn genetic diseases | Uncertain significance (Oct 20, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RPH3AL | protein_coding | protein_coding | ENST00000331302 | 8 | 173753 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.44e-12 | 0.0526 | 125634 | 1 | 113 | 125748 | 0.000453 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.314 | 192 | 180 | 1.07 | 0.0000113 | 2003 |
Missense in Polyphen | 92 | 79.316 | 1.1599 | 846 | ||
Synonymous | 0.134 | 74 | 75.5 | 0.980 | 0.00000500 | 640 |
Loss of Function | 0.191 | 18 | 18.9 | 0.953 | 0.00000122 | 182 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00172 | 0.00172 |
Ashkenazi Jewish | 0.000895 | 0.000893 |
East Asian | 0.000435 | 0.000435 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000386 | 0.000360 |
Middle Eastern | 0.000435 | 0.000435 |
South Asian | 0.000795 | 0.000752 |
Other | 0.000327 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Rab GTPase effector involved in the late steps of regulated exocytosis, both in endocrine and exocrine cells (By similarity). Acts as a potential RAB3B effector protein in epithelial cells. {ECO:0000250, ECO:0000269|PubMed:15003533}.;
- Pathway
- Deregulation of Rab and Rab Effector Genes in Bladder Cancer
(Consensus)
Intolerance Scores
- loftool
- 0.175
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 42.16
Haploinsufficiency Scores
- pHI
- 0.186
- hipred
- N
- hipred_score
- 0.208
- ghis
- 0.502
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.921
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rph3al
- Phenotype
- endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; digestive/alimentary phenotype;
Gene ontology
- Biological process
- intracellular protein transport;exocytosis;regulation of calcium ion-dependent exocytosis;response to drug;glucose homeostasis;negative regulation of G protein-coupled receptor signaling pathway;positive regulation of protein secretion
- Cellular component
- cytoplasm;transport vesicle membrane;secretory granule membrane
- Molecular function
- protein binding;cytoskeletal protein binding;Rab GTPase binding;LIM domain binding;metal ion binding