STATH
protein-codingstatherin, the group of Histatins and statherin
Gene summary
Predicted to enable extracellular matrix constituent, lubricant activity and hydroxyapatite binding activity. Predicted to be a structural constituent of tooth enamel. Predicted to be involved in antimicrobial humoral immune response mediated by antimicrobial peptide and killing of cells of another organism. Predicted to be located in extracellular region. Predicted to be active in mitochondrion and obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to STATH variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003154.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 10 | 1 | 11 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 0 | 11 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003145.1 | 4 | MANE Select | |
| Ensembl | ENSP00000246895.4 | 4 | MANE Select | |
| RefSeq | NP_001009181.1 | 3 | Standard | |
| Ensembl | ENSP00000370448.2 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Salivary secretion - Homo sapiens (human)
Biological Process
- ossification
- negative regulation of bone mineralization
- biomineral tissue development
- defense response to bacterium
- saliva secretion
Molecular Function
- protein binding
- extracellular matrix constituent, lubricant activity
- structural constituent of tooth enamel
- hydroxyapatite binding
Cellular Component
- extracellular region
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000246895
- Coding exons
- 4
- Length
- 6641
- Individuals with no LoFs
- 125371
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 300
- Defined
- 125673
- p
- 0.00120
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.306 | 38 | 33.1 | 1.15 | 0.00000167 | 392 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.015 | 0.015 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0.00043 | 0.00042 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
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.;
Intolerance Scores
- LoFtool
- 0.551
- RVIS EVS
- 0.3
- RVIS percentile EVS
- 71.81
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |