HTN3

Chr 4

histatin 3

Also known as: HIS2, HTN2, HTN5, Hst 3, PB

NCBI Gene: 3347ENSG00000205649UniProt: P15516

HTN3 encodes histatin-3, a small histidine-rich cationic protein found in saliva that functions as an antimicrobial peptide with antibacterial and antifungal activities, and contributes to wound healing and formation of the protective enamel pellicle on tooth surfaces. Based on the available data, no human diseases have been definitively associated with HTN3 mutations. An inheritance pattern cannot be determined from the current information.

ResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 1.89
Clinical Summary— HTN3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
23 unique Pathogenic / Likely Pathogenic· 11 VUS of 38 total submissions
Explore recent and relevant literature in Research Assistant →
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.89LOEUF
pLI 0.000
Z-score -0.47
OE 1.23 (0.65–1.89)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.47Z-score
OE missense 1.27 (0.95–1.70)
31 obs / 24.5 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE1.23 (0.65–1.89)
0≤0.351.4
Missense OE1.27 (0.95–1.70)
0≤0.61.4
Synonymous OE1.37
0≤1.21.6
LoF obs/exp: 6 / 4.9Missense obs/exp: 31 / 24.5Syn Z: -0.78
DN
0.88top 5%
GOF
0.5465th %ile
LOF
0.1796th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

38 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic22
Likely Pathogenic1
VUS11
Likely Benign3
Benign1
22
Pathogenic
1
Likely Pathogenic
11
VUS
3
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
0
21
0
22
Likely Pathogenic
0
0
1
0
1
VUS
0
3
8
0
11
Likely Benign
0
1
2
0
3
Benign
0
1
0
0
1
Total1532038

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

HTN3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients