RIMS3

regulating synaptic membrane exocytosis 3, the group of Regulating synaptic membrane exocytosis family

Basic information

Region (hg38): 1:40620679-40665682

Links

ENSG00000117016 ∙ NCBI:9783 ∙ OMIM:611600 ∙ HGNC:21292 ∙ Uniprot:Q9UJD0 ∙ 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 RIMS3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RIMS3 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				4	2	6
missense			23	2	2	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	23	7	5

Variants in RIMS3

This is a list of pathogenic ClinVar variants found in the RIMS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-40626545-T-C		not specified	Uncertain significance (Jan 10, 2022)
1-40626578-G-T		not specified	Uncertain significance (Apr 20, 2024)
1-40626638-G-A		not specified	Uncertain significance (Jan 31, 2023)
1-40626639-C-T		not specified	Uncertain significance (Aug 16, 2021)
1-40626683-A-G		not specified	Uncertain significance (Mar 07, 2023)
1-40626701-A-C		not specified	Uncertain significance (Oct 13, 2023)
1-40626705-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-40628824-C-T		RIMS3-related disorder	Likely benign (May 10, 2022)
1-40628866-G-A		not specified	Uncertain significance (Sep 29, 2022)
1-40628882-G-T		RIMS3-related disorder	Benign (Jun 17, 2019)
1-40628905-C-T		RIMS3-related disorder	Benign (Nov 16, 2019)
1-40628943-T-C		not specified	Uncertain significance (Nov 22, 2023)
1-40629292-G-C		RIMS3-related disorder	Benign (May 28, 2019)
1-40629334-G-C		not specified	Uncertain significance (Jan 29, 2024)
1-40629338-G-T		RIMS3-related disorder	Likely benign (Jun 23, 2021)
1-40629358-C-T		not specified	Uncertain significance (Nov 07, 2022)
1-40633070-C-T		not specified	Uncertain significance (Aug 15, 2023)
1-40635900-A-G			Benign (Oct 16, 2021)
1-40635919-C-T		not specified	Uncertain significance (Jan 31, 2023)
1-40635920-C-T		not specified	Uncertain significance (Mar 18, 2024)
1-40635924-G-A		RIMS3-related disorder	Likely benign (Dec 16, 2022)
1-40635925-G-A		not specified	Uncertain significance (Jul 12, 2023)
1-40635989-G-A		not specified	Uncertain significance (Aug 14, 2023)
1-40635999-C-T		RIMS3-related disorder	Likely benign (Jun 21, 2019)
1-40636001-C-T		not specified	Uncertain significance (Jan 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RIMS3	protein_coding	protein_coding	ENST00000372684	6	44979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000149	0.878	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.974	162	201	0.807	0.0000134	1980
Missense in Polyphen		60	82.412	0.72805		826
Synonymous	1.20	68	81.9	0.831	0.00000544	650
Loss of Function	1.41	8	13.6	0.587	7.70e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000530	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates synaptic membrane exocytosis. {ECO:0000250}.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.512
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.384
• hipred: N
• hipred_score: 0.455
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.812

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rims3
• Phenotype: hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: calcium ion regulated exocytosis;regulation of membrane potential;regulation of synaptic plasticity;calcium ion-regulated exocytosis of neurotransmitter;positive regulation of synaptic transmission;regulation of synaptic vesicle exocytosis
• Cellular component: cell junction;presynaptic membrane;synapse;presynaptic active zone;cytoskeleton of presynaptic active zone;presynaptic active zone cytoplasmic component
• Molecular function: Rab GTPase binding;ion channel binding