GeneBe

SGSM3

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

Basic information

Region (hg38): 22:40370591-40410289

Previous symbols: [ "RUTBC3" ]

Links

ENSG00000100359 ∙ NCBI:27352 ∙ OMIM:610440 ∙ HGNC:25228 ∙ Uniprot:Q96HU1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • intellectual disability (Limited), mode of inheritance: AR
  • neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SGSM3 gene.

  • not_specified (124 variants)
  • not_provided (21 variants)
  • EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
  • Autism (1 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. These statistics are base on transcript: NM_000015705.6. 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
10
clinvar
3
clinvar
 13
missense
124
clinvar
6
clinvar
1
clinvar
 131
nonsense
0
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
0
Total 0 1 124 16 4

Highest pathogenic variant AF is 0.00019862222

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SGSM3protein_codingprotein_codingENST00000248929 2139699
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
3.41e-150.87512558701611257480.000640
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1624754850.9790.00003284833
Missense in Polyphen140169.050.828141754
Synonymous-1.722442121.150.00001511504
Loss of Function2.093045.10.6650.00000228475

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006400.000637
Ashkenazi Jewish0.009580.00827
East Asian0.0003850.000381
Finnish0.00004710.0000462
European (Non-Finnish)0.0003770.000369
Middle Eastern0.0003850.000381
South Asian0.0002670.000261
Other0.001040.000978

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sgsm3
Phenotype

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