SGSM2

small G protein signaling modulator 2, the group of Small G protein signaling modulators

Basic information

Region (hg38): 17:2337498-2381058

Previous symbols: [ "RUTBC1" ]

Links

ENSG00000141258 ∙ NCBI:9905 ∙ OMIM:611418 ∙ HGNC:29026 ∙ Uniprot:O43147 ∙ 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 SGSM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGSM2 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					2	2
missense			69		2	71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	69	0	4

Variants in SGSM2

This is a list of pathogenic ClinVar variants found in the SGSM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-2337693-G-T		not specified	Uncertain significance (Apr 01, 2024)
17-2337704-G-A		not specified	Uncertain significance (Oct 26, 2022)
17-2337715-A-C		not specified	Uncertain significance (Jan 10, 2023)
17-2343560-G-A		not specified	Uncertain significance (Oct 13, 2023)
17-2361678-G-A		not specified	Uncertain significance (Mar 23, 2022)
17-2361679-C-T		not specified	Uncertain significance (Aug 16, 2022)
17-2361693-C-T		not specified	Uncertain significance (Feb 13, 2023)
17-2361694-G-A		not specified	Uncertain significance (Oct 17, 2023)
17-2361711-G-A		not specified	Uncertain significance (May 18, 2023)
17-2361739-G-C			Benign (Dec 28, 2017)
17-2361742-C-T		not specified	Uncertain significance (Feb 28, 2023)
17-2361769-T-C		not specified	Uncertain significance (Jan 03, 2024)
17-2362114-C-T		not specified	Uncertain significance (Aug 02, 2021)
17-2362129-A-C		not specified	Uncertain significance (Sep 14, 2022)
17-2362242-G-T		not specified	Uncertain significance (Jul 19, 2023)
17-2362851-A-G		not specified	Uncertain significance (Apr 27, 2024)
17-2363025-C-G		not specified	Uncertain significance (May 08, 2023)
17-2363048-C-T		not specified	Uncertain significance (Nov 27, 2023)
17-2363073-G-A		not specified	Uncertain significance (Feb 23, 2023)
17-2363120-C-T		not specified	Uncertain significance (Jan 20, 2023)
17-2363485-C-G		not specified	Uncertain significance (Jun 07, 2023)
17-2363519-G-A		not specified	Uncertain significance (Apr 12, 2024)
17-2363522-C-T		not specified	Uncertain significance (Jan 10, 2023)
17-2363556-G-A		not specified	Uncertain significance (Dec 14, 2023)
17-2363562-G-A		not specified	Uncertain significance (May 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SGSM2	protein_coding	protein_coding	ENST00000268989	24	43561

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.29e-9	1.00	125665	0	83	125748	0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.299	649	671	0.967	0.0000441	6840
Missense in Polyphen		149	195.88	0.76066		1973
Synonymous	-1.49	316	284	1.11	0.0000202	2039
Loss of Function	3.95	24	55.9	0.430	0.00000265	633

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000594	0.000594
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000498	0.000489
Finnish	0.000294	0.000277
European (Non-Finnish)	0.000321	0.000308
Middle Eastern	0.000498	0.000489
South Asian	0.000431	0.000425
Other	0.000188	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possesses GTPase activator activity towards RAB32, RAB33B and RAB38 (PubMed:26620560, PubMed:21808068). Regulates the trafficking of melanogenic enzymes TYR, TYRP1 and DCT/TYRP2 to melanosomes in melanocytes by inactivating RAB32 and RAB38. Inhibits RAB32 and RAB38 activation both directly by promoting their GTPase activity and indirectly by disrupting the RAB9A-HPS4 interaction which is required for RAB32/38 activation (PubMed:26620560). {ECO:0000269|PubMed:21808068, ECO:0000269|PubMed:26620560}.

Recessive Scores

• pRec: 0.0990

Intolerance Scores

• loftool: 0.760
• rvis_EVS: -0.74
• rvis_percentile_EVS: 13.8

Haploinsufficiency Scores

• pHI: 0.257
• hipred: N
• hipred_score: 0.414
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.792

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sgsm2

Gene ontology

• Biological process: intracellular protein transport;late endosome to Golgi transport;positive regulation of GTPase activity;activation of GTPase activity
• Cellular component: cytoplasm;melanosome
• Molecular function: GTPase activator activity;Rab GTPase binding