HTN1

histatin 1, the group of Histatins and statherin

Basic information

Region (hg38): 4:70050438-70058848

Links

ENSG00000126550 ∙ NCBI:3346 ∙ OMIM:142701 ∙ HGNC:5283 ∙ Uniprot:P15515 ∙ 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 HTN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTN1 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			4		1	5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	1

Variants in HTN1

This is a list of pathogenic ClinVar variants found in the HTN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-70053115-G-A		not specified	Uncertain significance (May 18, 2022)
4-70054325-G-A		not specified	Uncertain significance (Dec 27, 2022)
4-70054335-A-G		not specified	Uncertain significance (Jun 05, 2024)
4-70055510-T-C			Benign (Dec 31, 2019)
4-70055532-A-C		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTN1	protein_coding	protein_coding	ENST00000511674	4	8444

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0423	0.676	125427	0	63	125490	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.850	41	28.3	1.45	0.00000134	372
Missense in Polyphen		9	4.4226	2.035		57
Synonymous	-0.515	11	9.03	1.22	3.90e-7	87
Loss of Function	0.518	2	2.96	0.675	1.25e-7	40

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000673	0.000634
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000475	0.0000462
European (Non-Finnish)	0.000450	0.000414
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000183	0.000164

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.
• Pathway: Salivary secretion - Homo sapiens (human);Antimicrobial peptides;Innate Immune System;Immune System (Consensus)

Intolerance Scores

• loftool: 0.753
• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.79

Haploinsufficiency Scores

• pHI: 0.0287
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.291

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