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GeneBe

RPH3AL

rabphilin 3A like (without C2 domains)

Basic information

Region (hg38): 17:212388-386254

Links

ENSG00000181031NCBI:9501OMIM:604881HGNC:10296Uniprot:Q9UNE2AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPH3AL gene.

  • 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)link
17-215680-G-A Inborn genetic diseases Uncertain significance (Apr 25, 2022)link
17-215710-T-A Inborn genetic diseases Uncertain significance (Sep 07, 2022)link
17-215712-C-A Inborn genetic diseases Uncertain significance (Aug 10, 2021)link
17-215721-C-G Inborn genetic diseases Uncertain significance (Apr 07, 2023)link
17-215758-C-T Inborn genetic diseases Likely benign (Apr 11, 2023)link
17-215763-G-A Inborn genetic diseases Uncertain significance (Nov 08, 2022)link
17-215787-G-A Inborn genetic diseases Uncertain significance (Sep 16, 2021)link
17-219653-G-A Inborn genetic diseases Uncertain significance (Feb 07, 2023)link
17-219659-T-C Inborn genetic diseases Uncertain significance (Jun 29, 2023)link
17-219662-C-A Inborn genetic diseases Uncertain significance (Oct 03, 2022)link
17-219721-C-T Inborn genetic diseases Uncertain significance (Jul 22, 2022)link
17-247173-G-A Inborn genetic diseases Uncertain significance (Apr 07, 2022)link
17-247200-G-A Inborn genetic diseases Uncertain significance (Dec 28, 2022)link
17-247212-C-T Inborn genetic diseases Uncertain significance (Dec 13, 2022)link
17-247221-G-A Inborn genetic diseases Uncertain significance (Aug 10, 2021)link
17-247249-G-A Inborn genetic diseases Uncertain significance (Jan 24, 2023)link
17-247269-C-T Inborn genetic diseases Uncertain significance (Mar 06, 2023)link
17-247272-G-C Inborn genetic diseases Uncertain significance (Dec 20, 2021)link
17-251083-A-G Inborn genetic diseases Uncertain significance (May 09, 2023)link
17-252336-C-T Inborn genetic diseases Uncertain significance (Nov 01, 2022)link
17-252338-A-G Inborn genetic diseases Uncertain significance (Mar 01, 2023)link
17-252354-C-T Inborn genetic diseases Uncertain significance (Jun 28, 2022)link
17-327489-G-A Inborn genetic diseases Uncertain significance (Sep 13, 2023)link
17-327519-C-T Inborn genetic diseases Uncertain significance (Oct 20, 2021)link

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPH3ALprotein_codingprotein_codingENST00000331302 8173753
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.44e-120.052612563411131257480.000453
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.3141921801.070.00001132003
Missense in Polyphen9279.3161.1599846
Synonymous0.1347475.50.9800.00000500640
Loss of Function0.1911818.90.9530.00000122182

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001720.00172
Ashkenazi Jewish0.0008950.000893
East Asian0.0004350.000435
Finnish0.000.00
European (Non-Finnish)0.0003860.000360
Middle Eastern0.0004350.000435
South Asian0.0007950.000752
Other0.0003270.000326

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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