RIMS4

regulating synaptic membrane exocytosis 4, the group of Regulating synaptic membrane exocytosis family

Basic information

Region (hg38): 20:44751808-44810546

Previous symbols: [ "C20orf190" ]

Links

ENSG00000101098 ∙ NCBI:140730 ∙ OMIM:611601 ∙ HGNC:16183 ∙ Uniprot:Q9H426 ∙ 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 RIMS4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RIMS4 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	1

Variants in RIMS4

This is a list of pathogenic ClinVar variants found in the RIMS4 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-44756215-G-C		not specified	Uncertain significance (Sep 25, 2023)
20-44756256-C-T		not specified	Uncertain significance (Mar 07, 2024)
20-44756328-G-A		not specified	Uncertain significance (May 08, 2024)
20-44757696-G-A		not specified	Uncertain significance (Jul 27, 2021)
20-44758099-G-A		not specified	Uncertain significance (Apr 30, 2024)
20-44758124-G-T		not specified	Uncertain significance (Jul 20, 2021)
20-44771368-G-A		not specified	Uncertain significance (Feb 10, 2023)
20-44771403-C-T			Benign (Dec 31, 2019)
20-44810180-T-G		not specified	Uncertain significance (Sep 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RIMS4	protein_coding	protein_coding	ENST00000541604	6	58531

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.233	0.761	125630	0	2	125632	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.89	63	168	0.374	0.0000103	1726
Missense in Polyphen		29	92.738	0.31271		901
Synonymous	1.05	63	74.5	0.846	0.00000482	559
Loss of Function	2.34	3	11.6	0.258	4.93e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000620	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000903	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.105
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.278
• hipred: Y
• hipred_score: 0.768
• ghis: 0.699

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.323

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rims4
• Phenotype: growth/size/body region phenotype

Gene ontology

• Biological process: 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;synaptic membrane;presynaptic active zone cytoplasmic component
• Molecular function: Rab GTPase binding;ion channel binding