SGSM1

small G protein signaling modulator 1, the group of Small G protein signaling modulators

Basic information

Region (hg38): 22:24806169-24927578

Previous symbols: [ "RUTBC2" ]

Links

ENSG00000167037 ∙ NCBI:129049 ∙ OMIM:611417 ∙ HGNC:29410 ∙ Uniprot:Q2NKQ1 ∙ 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 SGSM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGSM1 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	3	4
missense			87	1		88
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	1		6
Total	0	0	92	3	3

Variants in SGSM1

This is a list of pathogenic ClinVar variants found in the SGSM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-24844969-T-G		not specified	Uncertain significance (Dec 28, 2022)
22-24847651-G-A		not specified	Uncertain significance (Jul 17, 2024)
22-24847660-G-A		not specified	Uncertain significance (Feb 13, 2024)
22-24847672-C-T		not specified	Uncertain significance (Oct 10, 2023)
22-24847697-A-G		not specified	Uncertain significance (Jun 16, 2023)
22-24847742-C-T		not specified	Uncertain significance (Sep 08, 2024)
22-24847751-A-G		not specified	Uncertain significance (Sep 22, 2023)
22-24850283-A-C		not specified	Uncertain significance (Nov 21, 2023)
22-24850296-G-T		not specified	Uncertain significance (Sep 20, 2023)
22-24850374-A-G		not specified	Uncertain significance (May 20, 2024)
22-24855314-A-G		not specified	Uncertain significance (Feb 28, 2023)
22-24855315-T-A		not specified	Uncertain significance (Feb 28, 2023)
22-24855335-T-C		not specified	Uncertain significance (Nov 13, 2024)
22-24855375-G-A		not specified	Uncertain significance (Jan 22, 2024)
22-24855392-G-A		not specified	Uncertain significance (Oct 12, 2024)
22-24855392-G-T		not specified	Likely benign (Nov 07, 2024)
22-24855411-C-A		not specified	Uncertain significance (Jun 21, 2022)
22-24855549-A-G		not specified	Uncertain significance (Jul 09, 2021)
22-24855585-C-T		not specified	Uncertain significance (Feb 15, 2023)
22-24855603-C-T		not specified	Uncertain significance (Dec 08, 2021)
22-24855636-C-T		not specified	Uncertain significance (Oct 19, 2024)
22-24855637-G-A		not specified	Uncertain significance (Oct 14, 2023)
22-24855679-C-T		not specified	Uncertain significance (Aug 10, 2024)
22-24859716-A-G		not specified	Uncertain significance (Jun 07, 2023)
22-24859722-G-A		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SGSM1	protein_coding	protein_coding	ENST00000400359	26	121310

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000160	1.00	125649	0	43	125692	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.97	556	703	0.791	0.0000438	7563
Missense in Polyphen		137	208.44	0.65727		2196
Synonymous	0.0423	293	294	0.997	0.0000201	2183
Loss of Function	4.80	20	60.2	0.332	0.00000292	670

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000314	0.000308
Ashkenazi Jewish	0.00	0.00
East Asian	0.000224	0.000217
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000192	0.000185
Middle Eastern	0.000224	0.000217
South Asian	0.000207	0.000196
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interacts with numerous Rab family members, functioning as Rab effector for some, and as GTPase activator for others. Promotes GTP hydrolysis by RAB34 and RAB36. Probably functions as GTPase effector with RAB9A and RAB9B; does not stimulate GTP hydrolysis with RAB9A and RAB9B. {ECO:0000269|PubMed:22637480}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.661
• rvis_EVS: -0.7
• rvis_percentile_EVS: 14.83

Haploinsufficiency Scores

• pHI: 0.199
• hipred: Y
• hipred_score: 0.639
• ghis: 0.601

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.285

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sgsm1
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: intracellular protein transport;activation of GTPase activity
• Cellular component: cytoplasm;Golgi apparatus;cytosol;cytoplasmic vesicle membrane
• Molecular function: GTPase activator activity;Rab GTPase binding