RPH3AL

rabphilin 3A like (without C2 domains)

Basic information

Region (hg38): 17:212389-386254

Links

ENSG00000181031 ∙ NCBI:9501 ∙ OMIM:604881 ∙ HGNC:10296 ∙ Uniprot:Q9UNE2 ∙ 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 RPH3AL gene.

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.

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				1		1
missense			38	3		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	3		8
Total	0	0	43	7	0

Variants in RPH3AL

This is a list of pathogenic ClinVar variants found in the RPH3AL region.

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

Position	Type	Phenotype	Significance	ClinVar
17-213884-C-A		not specified	Uncertain significance (Oct 06, 2023)
17-213896-C-T		not specified	Uncertain significance (Jun 11, 2021)
17-215655-G-A		not specified	Likely benign (Dec 14, 2022)
17-215675-G-A			Likely benign (May 01, 2023)
17-215680-G-A		not specified	Uncertain significance (Nov 24, 2024)
17-215683-G-C		not specified	Uncertain significance (Jan 31, 2024)
17-215694-G-A		not specified	Uncertain significance (Nov 24, 2021)
17-215710-T-A		not specified	Uncertain significance (Sep 07, 2022)
17-215712-C-A		not specified	Uncertain significance (Aug 10, 2021)
17-215721-C-G		not specified	Uncertain significance (Apr 07, 2023)
17-215758-C-T		not specified	Likely benign (Apr 11, 2023)
17-215763-G-A		not specified	Uncertain significance (Nov 08, 2022)
17-215787-G-A		not specified	Uncertain significance (Sep 16, 2021)
17-219653-G-A		not specified	Uncertain significance (Feb 07, 2023)
17-219659-T-C		not specified	Uncertain significance (Jun 29, 2023)
17-219662-C-A		not specified	Uncertain significance (Oct 03, 2022)
17-219665-C-T		not specified	Uncertain significance (Jun 10, 2024)
17-219694-G-C		not specified	Uncertain significance (Feb 27, 2024)
17-219721-C-T		not specified	Uncertain significance (Jul 22, 2022)
17-247138-G-A		not specified	Uncertain significance (Dec 14, 2022)
17-247173-G-A		not specified	Uncertain significance (Apr 07, 2022)
17-247200-G-A		not specified	Uncertain significance (Dec 28, 2022)
17-247202-G-T		not specified	Uncertain significance (Jul 14, 2024)
17-247212-C-T		not specified	Uncertain significance (Dec 13, 2022)
17-247221-G-A		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

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: 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

	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