STATH
Basic information
Region (hg38): 4:69995966-70002570
Links
Phenotypes
GenCC
Source:
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 STATH 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 | 0 | |||||
| missense | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 1 | 0 |
Variants in STATH
This is a list of pathogenic ClinVar variants found in the STATH region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-69998448-T-C | Likely benign (Apr 16, 2018) | |||
| 4-69998484-T-C | not specified | Uncertain significance (Dec 05, 2024) | ||
| 4-69999816-G-A | Benign (Feb 27, 2018) | |||
| 4-70000869-T-C | not specified | Uncertain significance (Feb 04, 2025) | ||
| 4-70000888-T-C | not specified | Uncertain significance (Feb 06, 2023) | ||
| 4-70000909-C-A | not specified | Uncertain significance (Nov 08, 2021) | ||
| 4-70000941-A-G | not specified | Uncertain significance (Sep 26, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STATH | protein_coding | protein_coding | ENST00000246895 | 4 | 6641 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000798 | 0.329 | 125371 | 2 | 300 | 125673 | 0.00120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.306 | 38 | 33.1 | 1.15 | 0.00000167 | 392 |
| Missense in Polyphen | 4 | 1.8054 | 2.2155 | 31 | ||
| Synonymous | -1.65 | 18 | 11.0 | 1.63 | 5.39e-7 | 108 |
| Loss of Function | -0.0981 | 6 | 5.75 | 1.04 | 2.43e-7 | 68 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000203 | 0.000203 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0151 | 0.0151 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000266 | 0.0000264 |
| Middle Eastern | 0.0151 | 0.0151 |
| South Asian | 0.000427 | 0.000425 |
| Other | 0.000490 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Salivary protein that stabilizes saliva supersaturated with calcium salts by inhibiting the precipitation of calcium phosphate salts. It also modulates hydroxyapatite crystal formation on the tooth surface.;
- Pathway
- Salivary secretion - Homo sapiens (human)
(Consensus)
Intolerance Scores
- loftool
- 0.551
- rvis_EVS
- 0.3
- rvis_percentile_EVS
- 71.81
Haploinsufficiency Scores
- pHI
- 0.0679
- hipred
- N
- hipred_score
- 0.146
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- ossification;negative regulation of bone mineralization;biomineral tissue development;defense response to bacterium;saliva secretion
- Cellular component
- extracellular region
- Molecular function
- protein binding;extracellular matrix constituent, lubricant activity;structural constituent of tooth enamel;hydroxyapatite binding