RGS3

regulator of G protein signaling 3, the group of PDZ domain containing|Regulators of G-protein signaling|C2 domain containing

Basic information

Region (hg38): 9:113444731-113597743

Links

ENSG00000138835 ∙ NCBI:5998 ∙ OMIM:602189 ∙ HGNC:9999 ∙ Uniprot:P49796 ∙ 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 RGS3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGS3 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	2
missense			94	7	1	102
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	95	8	2

Variants in RGS3

This is a list of pathogenic ClinVar variants found in the RGS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-113461736-A-G		not specified	Likely benign (Sep 17, 2021)
9-113461775-G-T		not specified	Uncertain significance (Apr 08, 2024)
9-113462027-C-T		not specified	Uncertain significance (May 18, 2022)
9-113462034-C-G		not specified	Uncertain significance (Aug 12, 2021)
9-113462048-C-T		not specified	Uncertain significance (Dec 06, 2021)
9-113462090-C-T		not specified	Uncertain significance (Sep 22, 2023)
9-113462199-C-T		not specified	Uncertain significance (Oct 09, 2024)
9-113479508-A-G		not specified	Uncertain significance (Feb 03, 2022)
9-113483074-G-A		not specified	Uncertain significance (Apr 12, 2022)
9-113483074-G-T		not specified	Uncertain significance (Sep 04, 2024)
9-113483107-C-T		not specified	Uncertain significance (Dec 05, 2022)
9-113483116-A-C		not specified	Uncertain significance (Mar 30, 2024)
9-113484181-C-T		not specified	Uncertain significance (Nov 09, 2024)
9-113484189-G-A		not specified	Likely benign (Sep 15, 2022)
9-113495787-C-G		not specified	Uncertain significance (Oct 20, 2024)
9-113495829-C-T		not specified	Uncertain significance (Aug 20, 2023)
9-113497356-C-T		not specified	Uncertain significance (Jan 09, 2024)
9-113497383-C-T		not specified	Uncertain significance (Jun 09, 2022)
9-113497392-C-T		not specified	Uncertain significance (Jun 13, 2024)
9-113497396-C-T		not specified	Likely benign (Nov 13, 2023)
9-113498048-G-A		not specified	Uncertain significance (Feb 21, 2024)
9-113505476-T-C		not specified	Uncertain significance (Nov 15, 2023)
9-113505490-G-A		not specified	Uncertain significance (Dec 01, 2022)
9-113506393-C-A		not specified	Uncertain significance (Feb 14, 2023)
9-113507306-A-T		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGS3	protein_coding	protein_coding	ENST00000374140	25	153008

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.26e-11	1.00	125636	0	112	125748	0.000445

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	635	712	0.891	0.0000438	7750
Missense in Polyphen		197	257.25	0.7658		2709
Synonymous	-0.194	302	298	1.01	0.0000189	2418
Loss of Function	3.78	28	59.5	0.471	0.00000286	702

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000581	0.000581
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00104	0.000979
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000491	0.000484
Middle Eastern	0.00104	0.000979
South Asian	0.000604	0.000588
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Down-regulates signaling from heterotrimeric G-proteins by increasing the GTPase activity of the alpha subunits, thereby driving them into their inactive GDP-bound form. Down-regulates G- protein-mediated release of inositol phosphates and activation of MAP kinases. {ECO:0000269|PubMed:10749886, ECO:0000269|PubMed:11294858, ECO:0000269|PubMed:8602223, ECO:0000269|PubMed:9858594}.
• Pathway: Axon guidance - Homo sapiens (human);Myometrial Relaxation and Contraction Pathways;Calcium Regulation in the Cardiac Cell;Signaling by GPCR;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;Ephrin B reverse signaling;GPCR signaling-G alpha i;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.909
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.17

Haploinsufficiency Scores

• pHI: 0.275
• hipred: Y
• hipred_score: 0.522
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rgs3
• Phenotype: immune system phenotype; hematopoietic system phenotype; respiratory system phenotype

Zebrafish Information Network

• Gene name: rgs3a
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: inactivation of MAPK activity;regulation of G protein-coupled receptor signaling pathway;positive regulation of GTPase activity
• Cellular component: nucleoplasm;cytosol;plasma membrane
• Molecular function: GTPase activator activity;protein binding