HTN3

histatin 3, the group of Histatins and statherin

Basic information

Region (hg38): 4:70028455-70036538

Links

ENSG00000205649 ∙ NCBI:3347 ∙ OMIM:142702 ∙ HGNC:5284 ∙ Uniprot:P15516 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HTN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTN3 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			1	1	1	3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	1	1

Variants in HTN3

This is a list of pathogenic ClinVar variants found in the HTN3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-70030780-C-A		not specified	Uncertain significance (Oct 10, 2023)
4-70030790-C-T		not specified	Likely benign (Oct 10, 2023)
4-70033186-G-A		-	no classification for the single variant (-)
4-70033188-G-C			Benign (Dec 31, 2019)
4-70033205-T-A		-	no classification for the single variant (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTN3	protein_coding	protein_coding	ENST00000530128	4	8126

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000411	0.235	123271	167	2264	125702	0.00972

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.469	31	24.5	1.27	0.00000104	327
Missense in Polyphen		3	4.0898	0.73353		60
Synonymous	-0.781	10	7.31	1.37	3.13e-7	76
Loss of Function	-0.473	6	4.87	1.23	2.69e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.155	0.150
Ashkenazi Jewish	0.0000996	0.0000993
East Asian	0.000712	0.000707
Finnish	0.00	0.00
European (Non-Finnish)	0.000258	0.000255
Middle Eastern	0.000712	0.000707
South Asian	0.000303	0.000294
Other	0.00318	0.00310

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histatins are salivary proteins that are considered to be major precursors of the protective proteinaceous structure on tooth surfaces (enamel pellicle). In addition, histatins exhibit antibacterial and antifungal activities. His3-(20-43)-peptide (histatin-5) is especially effective against C.albicans and C.neoformans, and inhibits Lys-gingipain and Arg-gingipain (rgpB) from P.gingivalis. In addition, His3-(20-43)-peptide is a potent inhibitor of metalloproteinases MMP2 and MMP9. {ECO:0000269|PubMed:11179305, ECO:0000269|PubMed:8945538}.
• Pathway: Salivary secretion - Homo sapiens (human);Antimicrobial peptides;Innate Immune System;Immune System (Consensus)

Intolerance Scores

• loftool: 0.741
• rvis_EVS: 0.95
• rvis_percentile_EVS: 89.91

Haploinsufficiency Scores

• pHI: 0.0505
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.102

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: antimicrobial humoral response;biomineral tissue development;killing of cells of other organism;defense response to bacterium;defense response to fungus
• Cellular component: extracellular region
• Molecular function: protein binding;metal ion binding