SGTA
small glutamine rich tetratricopeptide repeat co-chaperone alpha, the group of Tetratricopeptide repeat domain containing|GET4-GET5 transmembrane domain recognition complex subunits
Basic information
Region (hg38): 19:2754715-2783362
Previous symbols: [ "SGT" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGTA 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 | |||||
| missense | 10 | 10 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 2 |
Variants in SGTA
This is a list of pathogenic ClinVar variants found in the SGTA region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-2757697-G-A | Uncertain significance (Aug 28, 2019) | |||
| 19-2757705-C-G | not specified | Uncertain significance (Apr 24, 2023) | ||
| 19-2757706-T-C | not specified | Uncertain significance (Aug 12, 2022) | ||
| 19-2757736-C-T | not specified | Uncertain significance (Jan 20, 2023) | ||
| 19-2757762-C-T | not specified | Uncertain significance (Dec 15, 2022) | ||
| 19-2757775-C-T | not specified | Uncertain significance (Jun 07, 2023) | ||
| 19-2759289-C-T | Benign (Jun 18, 2018) | |||
| 19-2765255-T-C | not specified | Uncertain significance (Dec 02, 2022) | ||
| 19-2765268-C-T | not specified | Uncertain significance (Nov 03, 2023) | ||
| 19-2767212-C-T | Benign (May 14, 2018) | |||
| 19-2767590-G-A | not specified | Uncertain significance (Apr 18, 2023) | ||
| 19-2767591-C-T | not specified | Uncertain significance (Apr 18, 2023) | ||
| 19-2767662-G-A | not specified | Uncertain significance (Aug 13, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SGTA | protein_coding | protein_coding | ENST00000221566 | 10 | 28658 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.946 | 0.0537 | 125721 | 0 | 5 | 125726 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.97 | 131 | 212 | 0.619 | 0.0000142 | 2058 |
| Missense in Polyphen | 24 | 62.477 | 0.38414 | 677 | ||
| Synonymous | -0.283 | 99 | 95.5 | 1.04 | 0.00000789 | 572 |
| Loss of Function | 3.50 | 2 | 18.0 | 0.111 | 8.66e-7 | 201 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000126 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000601 | 0.0000544 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000601 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Co-chaperone that binds misfolded and hydrophobic patches-containing client proteins in the cytosol. Mediates their targeting to the endoplasmic reticulum but also regulates their sorting to the proteasome when targeting fails (PubMed:28104892). Functions in tail-anchored/type II transmembrane proteins membrane insertion constituting with ASNA1 and the BAG6 complex a targeting module (PubMed:28104892). Functions upstream of the BAG6 complex and ASNA1, binding more rapidly the transmembrane domain of newly synthesized proteins (PubMed:28104892, PubMed:25535373). It is also involved in the regulation of the endoplasmic reticulum- associated misfolded protein catabolic process via its interaction with BAG6: collaborates with the BAG6 complex to maintain hydrophobic substrates in non-ubiquitinated states (PubMed:23129660, PubMed:25179605). Competes with RNF126 for interaction with BAG6, preventing the ubiquitination of client proteins associated with the BAG6 complex (PubMed:27193484). Binds directly to HSC70 and HSP70 and regulates their ATPase activity (PubMed:18759457). {ECO:0000269|PubMed:18759457, ECO:0000269|PubMed:23129660, ECO:0000269|PubMed:25179605, ECO:0000269|PubMed:25535373, ECO:0000269|PubMed:27193484, ECO:0000269|PubMed:28104892}.;
Recessive Scores
- pRec
- 0.249
Intolerance Scores
- loftool
- 0.0715
- rvis_EVS
- -0.67
- rvis_percentile_EVS
- 15.76
Haploinsufficiency Scores
- pHI
- 0.191
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.574
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.977
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sgta
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; renal/urinary system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Gene ontology
- Biological process
- posttranslational protein targeting to endoplasmic reticulum membrane;viral process;ubiquitin-dependent ERAD pathway;chaperone-mediated protein folding;tail-anchored membrane protein insertion into ER membrane;negative regulation of ER-associated ubiquitin-dependent protein catabolic process;positive regulation of ER-associated ubiquitin-dependent protein catabolic process;positive regulation of chaperone-mediated protein folding;negative regulation of ubiquitin-dependent protein catabolic process
- Cellular component
- nucleus;cytoplasm;cytosol;membrane;TRC complex;extrinsic component of synaptic vesicle membrane
- Molecular function
- protein binding;protein-containing complex scaffold activity;identical protein binding;protein self-association;BAT3 complex binding