SNTG1
Basic information
Region (hg38): 8:49909788-50796692
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (14 variants)
- not provided (5 variants)
- Gestational diabetes mellitus uncontrolled (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNTG1 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 | 1 | |||||
| missense | 14 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 1 | 1 | ||||
| non coding ? | 1 | |||||
| Total | 0 | 0 | 14 | 2 | 1 |
Variants in SNTG1
This is a list of pathogenic ClinVar variants found in the SNTG1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNTG1 | protein_coding | protein_coding | ENST00000522124 | 17 | 884330 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.163 | 0.837 | 125726 | 0 | 21 | 125747 | 0.0000835 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.329 | 289 | 274 | 1.06 | 0.0000140 | 3363 |
| Missense in Polyphen | 77 | 79.123 | 0.97317 | 971 | ||
| Synonymous | -2.44 | 132 | 101 | 1.31 | 0.00000537 | 970 |
| Loss of Function | 3.98 | 8 | 32.5 | 0.246 | 0.00000155 | 388 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000908 | 0.0000905 |
| Ashkenazi Jewish | 0.0000996 | 0.0000992 |
| East Asian | 0.000114 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000100 | 0.0000967 |
| Middle Eastern | 0.000114 | 0.000109 |
| South Asian | 0.000177 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Adapter protein that binds to and probably organizes the subcellular localization of a variety of proteins. May link various receptors to the actin cytoskeleton and the dystrophin glycoprotein complex (By similarity). May participate in regulating the subcellular location of diacylglycerol kinase-zeta to ensure that diacylglycerol is rapidly inactivated following receptor activation. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- loftool
- 0.639
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.74
Haploinsufficiency Scores
- pHI
- 0.226
- hipred
- Y
- hipred_score
- 0.604
- ghis
- 0.563
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.757
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sntg1
- Phenotype
Gene ontology
- Biological process
- cell communication
- Cellular component
- nucleus;cytoplasm;cytoskeleton;dystrophin-associated glycoprotein complex;syntrophin complex;ruffle membrane
- Molecular function
- actin binding;structural molecule activity;protein C-terminus binding