SGSM1
Basic information
Region (hg38): 22:24806169-24927578
Previous symbols: [ "RUTBC2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 5 | |||||
missense | 124 | 128 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 124 | 6 | 3 |
GnomAD
Source:
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:
- 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