SGSM3

small G protein signaling modulator 3, the group of Small G protein signaling modulators

Basic information

Region (hg38): 22:40370590-40410289

Previous symbols: [ "RUTBC3" ]

Links

ENSG00000100359 ∙ NCBI:27352 ∙ OMIM:610440 ∙ HGNC:25228 ∙ Uniprot:Q96HU1 ∙ 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 SGSM3 gene.

• Inborn genetic diseases (46 variants)
• not provided (16 variants)
• SGSM3-related intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGSM3 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				7	3	10
missense			44	4	1	49
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	1	44	11	5

Highest pathogenic variant AF is 0.000269

Variants in SGSM3

This is a list of pathogenic ClinVar variants found in the SGSM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-40401596-G-A		not specified	Uncertain significance (May 24, 2023)
22-40401617-C-T		not specified	Uncertain significance (Dec 08, 2023)
22-40401643-T-C			Benign (Feb 07, 2018)
22-40404267-A-C		not specified	Uncertain significance (Dec 14, 2023)
22-40404277-C-T		not specified	Uncertain significance (Dec 17, 2023)
22-40404300-G-A		not specified	Uncertain significance (Jan 05, 2022)
22-40404316-G-A		not specified	Uncertain significance (Apr 14, 2022)
22-40404360-G-A		not specified	Uncertain significance (Mar 24, 2023)
22-40404396-C-T			Likely benign (May 29, 2018)
22-40404567-G-A		not specified	Uncertain significance (Aug 22, 2022)
22-40404612-A-G		not specified	Uncertain significance (Dec 18, 2023)
22-40404614-C-T		not specified	Uncertain significance (Oct 12, 2022)
22-40404617-G-C		not specified	Uncertain significance (Feb 28, 2023)
22-40404632-A-G		not specified	Uncertain significance (Feb 28, 2023)
22-40404641-G-A		not specified	Uncertain significance (Aug 02, 2021)
22-40405147-A-C		not specified	Uncertain significance (Jan 10, 2023)
22-40405177-G-A		not specified	Uncertain significance (Feb 06, 2023)
22-40405186-G-A		not specified	Uncertain significance (Aug 17, 2022)
22-40405203-C-T			Benign (Jun 02, 2018)
22-40405204-G-A		not specified	Uncertain significance (Apr 13, 2022)
22-40405231-C-T		not specified	Uncertain significance (Nov 18, 2022)
22-40405232-G-A		not specified	Uncertain significance (Jun 27, 2023)
22-40405260-C-T			Likely benign (Jun 26, 2018)
22-40405684-G-C		not specified	Uncertain significance (Feb 28, 2023)
22-40405686-A-C		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SGSM3	protein_coding	protein_coding	ENST00000248929	21	39699

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.41e-15	0.875	125587	0	161	125748	0.000640

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.162	475	485	0.979	0.0000328	4833
Missense in Polyphen		140	169.05	0.82814		1754
Synonymous	-1.72	244	212	1.15	0.0000151	1504
Loss of Function	2.09	30	45.1	0.665	0.00000228	475

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000640	0.000637
Ashkenazi Jewish	0.00958	0.00827
East Asian	0.000385	0.000381
Finnish	0.0000471	0.0000462
European (Non-Finnish)	0.000377	0.000369
Middle Eastern	0.000385	0.000381
South Asian	0.000267	0.000261
Other	0.00104	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a cooperative role in NF2-mediated growth suppression of cells. {ECO:0000269|PubMed:15541357}.
• Pathway: Ectoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.792
• rvis_EVS: -2.45
• rvis_percentile_EVS: 1.01

Haploinsufficiency Scores

• pHI: 0.127
• hipred: Y
• hipred_score: 0.706
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.834

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sgsm3

Gene ontology

• Biological process: intracellular protein transport;cell cycle arrest;regulation of Rab protein signal transduction;Rap protein signal transduction;positive regulation of GTPase activity;positive regulation of protein catabolic process;plasma membrane to endosome transport;activation of GTPase activity;regulation of cilium assembly
• Cellular component: cytosol;gap junction
• Molecular function: GTPase activator activity;protein binding;Rab GTPase binding