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

ENSG00000167037NCBI:129049OMIM:611417HGNC:29410Uniprot:Q2NKQ1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SGSM1 gene.

  • not_specified (136 variants)
  • not_provided (4 variants)
  • EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

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. These statistics are base on transcript: NM_001098497.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
3
clinvar
5
missense
124
clinvar
4
clinvar
128
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 124 6 3
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SGSM1protein_codingprotein_codingENST00000400359 26121310
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00001601.001256490431256920.000171
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.975567030.7910.00004387563
Missense in Polyphen137208.440.657272196
Synonymous0.04232932940.9970.00002012183
Loss of Function4.802060.20.3320.00000292670

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003140.000308
Ashkenazi Jewish0.000.00
East Asian0.0002240.000217
Finnish0.0001410.000139
European (Non-Finnish)0.0001920.000185
Middle Eastern0.0002240.000217
South Asian0.0002070.000196
Other0.0001670.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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