RIC3

RIC3 acetylcholine receptor chaperone

Basic information

Region (hg38): 11:8106055-8169055

Links

ENSG00000166405 ∙ NCBI:79608 ∙ OMIM:610509 ∙ HGNC:30338 ∙ Uniprot:Q7Z5B4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Parkinson disease (Limited), mode of inheritance: AD
• movement disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RIC3 gene.

• Inborn genetic diseases (13 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RIC3 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						0
missense			13		1	14
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	1

Variants in RIC3

This is a list of pathogenic ClinVar variants found in the RIC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-8110831-C-A		not specified	Uncertain significance (May 22, 2023)
11-8110963-G-A		not specified	Uncertain significance (Mar 05, 2024)
11-8110976-A-T		not specified	Uncertain significance (Apr 24, 2023)
11-8111048-T-C		not specified	Uncertain significance (Jan 05, 2022)
11-8111062-T-C		not specified	Uncertain significance (May 06, 2022)
11-8111081-G-T		not specified	Uncertain significance (Oct 12, 2021)
11-8126719-T-C		not specified	Uncertain significance (Aug 14, 2023)
11-8126740-C-A			Benign (Nov 09, 2018)
11-8126764-G-A		not specified	Uncertain significance (Feb 22, 2023)
11-8138283-T-G		not specified	Uncertain significance (Dec 13, 2023)
11-8138341-T-C		not specified	Uncertain significance (Jan 31, 2024)
11-8139983-A-G		not specified	Uncertain significance (Jan 17, 2024)
11-8140019-A-G		not specified	Uncertain significance (May 16, 2023)
11-8140049-C-T		not specified	Uncertain significance (Jan 26, 2022)
11-8140072-T-TG			Uncertain significance (May 03, 2023)
11-8140122-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-8140149-G-T			Uncertain significance (Sep 26, 2016)
11-8140156-G-T		not specified	Uncertain significance (Jul 10, 2023)
11-8168907-A-C		not specified	Uncertain significance (Jul 25, 2023)
11-8168914-C-A		not specified	Uncertain significance (Jan 30, 2024)
11-8168916-T-C		RIC3-related disorder	Likely benign (Jan 12, 2023)
11-8168961-G-A		not specified	Uncertain significance (Oct 17, 2023)
11-8168973-A-G		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RIC3	protein_coding	protein_coding	ENST00000309737	6	63006

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000214	0.723	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.640	220	195	1.13	0.00000954	2397
Missense in Polyphen		71	71.182	0.99744		897
Synonymous	-1.74	90	71.3	1.26	0.00000363	712
Loss of Function	1.16	11	16.0	0.687	8.50e-7	200

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000330	0.000329
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.0000544	0.0000544
South Asian	0.000329	0.000327
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes functional expression of homomeric alpha-7 and alpha-8 nicotinic acetylcholine receptors at the cell surface. May also promote functional expression of homomeric serotoninergic 5- HT3 receptors, and of heteromeric acetylcholine receptors alpha- 3/beta-2, alpha-3/beta-4, alpha-4/beta-2 and alpha-4/beta-4. {ECO:0000269|PubMed:12821669, ECO:0000269|PubMed:15504725, ECO:0000269|PubMed:15809299, ECO:0000269|PubMed:15927954, ECO:0000269|PubMed:16120769, ECO:0000269|PubMed:17609200, ECO:0000269|PubMed:18691158}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.385
• rvis_EVS: 1.62
• rvis_percentile_EVS: 96

Haploinsufficiency Scores

• pHI: 0.0974
• hipred: N
• hipred_score: 0.306
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.275

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ric3

Gene ontology

• Biological process: protein folding;positive regulation of cytosolic calcium ion concentration;synaptic transmission, cholinergic;protein localization to cell surface;cellular protein-containing complex assembly
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;integral component of membrane;neuron projection;neuronal cell body;intracellular membrane-bounded organelle
• Molecular function: acetylcholine receptor binding;protein folding chaperone