RPH3A

rabphilin 3A, the group of Synaptotagmin like tandem C2 proteins

Basic information

Region (hg38): 12:112570380-112898881

Links

ENSG00000089169 ∙ NCBI:22895 ∙ OMIM:612159 ∙ HGNC:17056 ∙ Uniprot:Q9Y2J0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital myasthenic syndrome (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPH3A gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPH3A 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				2	1	3
missense	1		38		1	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	38	2	2

Highest pathogenic variant AF is 0.0000131

Variants in RPH3A

This is a list of pathogenic ClinVar variants found in the RPH3A region.

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

Position	Type	Phenotype	Significance	ClinVar
12-112828349-A-G		Inborn genetic diseases	Uncertain significance (Mar 20, 2023)
12-112828352-C-G		Inborn genetic diseases	Uncertain significance (Apr 08, 2024)
12-112828353-G-T		Inborn genetic diseases	Uncertain significance (May 13, 2024)
12-112828373-C-T		Inborn genetic diseases	Uncertain significance (May 31, 2022)
12-112847722-C-A		Inborn genetic diseases	Uncertain significance (Apr 07, 2022)
12-112847727-G-T		Inborn genetic diseases	Uncertain significance (Jan 05, 2022)
12-112847746-G-A		Inborn genetic diseases	Uncertain significance (Oct 12, 2022)
12-112847764-C-G		Inborn genetic diseases	Uncertain significance (Jan 23, 2024)
12-112847790-A-G		Inborn genetic diseases	Uncertain significance (Jan 20, 2023)
12-112847841-G-A		not specified	Uncertain significance (Mar 04, 2019)
12-112865451-G-A		Inborn genetic diseases	Uncertain significance (Oct 03, 2023)
12-112865531-G-T		Inborn genetic diseases	Uncertain significance (Aug 02, 2023)
12-112866759-C-A		Inborn genetic diseases	Uncertain significance (May 13, 2024)
12-112866785-C-A		Inborn genetic diseases	Uncertain significance (Oct 29, 2021)
12-112866796-C-G		Inborn genetic diseases	Uncertain significance (Apr 07, 2023)
12-112868439-C-T		Inborn genetic diseases	Uncertain significance (Dec 13, 2023)
12-112868481-C-T		Inborn genetic diseases	Uncertain significance (Aug 02, 2023)
12-112868571-C-A		Inborn genetic diseases	Uncertain significance (Dec 27, 2022)
12-112868580-C-T		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
12-112868587-C-T		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
12-112868593-G-A			Benign (Dec 31, 2019)
12-112869751-T-G		RPH3A-related condition	Likely benign (Jun 21, 2024)
12-112869783-C-T		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
12-112869786-G-A		Inborn genetic diseases	Uncertain significance (Oct 03, 2022)
12-112869916-G-C		Inborn genetic diseases	Uncertain significance (May 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPH3A	protein_coding	protein_coding	ENST00000389385	20	328503

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00166	0.998	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	350	426	0.821	0.0000253	4532
Missense in Polyphen		89	147.28	0.60429		1564
Synonymous	0.172	152	155	0.982	0.00000922	1317
Loss of Function	4.39	14	46.2	0.303	0.00000268	479

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000621	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.000165	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein transport. Probably involved with Ras-related protein Rab-3A in synaptic vesicle traffic and/or synaptic vesicle fusion. Could play a role in neurotransmitter release by regulating membrane flow in the nerve terminal (By similarity). {ECO:0000250}.
• Pathway: Deregulation of Rab and Rab Effector Genes in Bladder Cancer (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.527
• rvis_EVS: -1.48
• rvis_percentile_EVS: 3.66

Haploinsufficiency Scores

• pHI: 0.302
• hipred: Y
• hipred_score: 0.597
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.699

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rph3a
• Phenotype: normal phenotype

Gene ontology

• Biological process: intracellular protein transport
• Cellular component: Golgi apparatus;cytosol;synaptic vesicle;extrinsic component of membrane;cell junction;secretory granule;synaptic vesicle membrane;protein-containing complex;neuron projection;synapse
• Molecular function: calcium ion binding;protein binding;calcium-dependent phospholipid binding;phosphatidylinositol-4,5-bisphosphate binding;zinc ion binding;selenium binding;Rab GTPase binding;phosphate ion binding;protein-containing complex binding;inositol 1,4,5 trisphosphate binding;phosphatidylinositol phosphate binding