HINT3

histidine triad nucleotide binding protein 3, the group of Histidine triad superfamily

Basic information

Region (hg38): 6:125956769-125980244

Links

ENSG00000111911 ∙ NCBI:135114 ∙ OMIM:609998 ∙ HGNC:18468 ∙ Uniprot:Q9NQE9 ∙ 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 HINT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HINT3 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in HINT3

This is a list of pathogenic ClinVar variants found in the HINT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-125957015-C-T		not specified	Uncertain significance (May 03, 2023)
6-125957062-G-A		not specified	Uncertain significance (Dec 13, 2023)
6-125957141-G-A		not specified	Uncertain significance (Feb 28, 2023)
6-125957143-C-T		not specified	Uncertain significance (Jun 12, 2023)
6-125957148-G-T		not specified	Uncertain significance (Jan 03, 2022)
6-125966915-T-C		not specified	Uncertain significance (Jul 12, 2023)
6-125966918-A-C		not specified	Uncertain significance (Jan 25, 2024)
6-125966923-G-T		not specified	Uncertain significance (Sep 26, 2022)
6-125966990-A-G		not specified	Uncertain significance (Jan 23, 2024)
6-125966993-A-G		not specified	Uncertain significance (Apr 22, 2024)
6-125972283-A-G		not specified	Uncertain significance (Feb 09, 2022)
6-125972315-T-A		not specified	Uncertain significance (Aug 12, 2021)
6-125972319-C-T		not specified	Uncertain significance (Jul 17, 2023)
6-125974866-C-G		not specified	Uncertain significance (May 26, 2022)
6-125974867-C-T		not specified	Uncertain significance (May 30, 2024)
6-125974954-A-G		not specified	Uncertain significance (May 27, 2022)
6-125977669-G-T		not specified	Uncertain significance (May 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HINT3	protein_coding	protein_coding	ENST00000229633	5	23461

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000348	0.207	125227	2	507	125736	0.00203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.594	82	98.6	0.832	0.00000434	1189
Missense in Polyphen		12	20.16	0.59524		256
Synonymous	0.614	33	37.8	0.873	0.00000175	342
Loss of Function	-0.192	8	7.43	1.08	3.12e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000970	0.000968
Ashkenazi Jewish	0.00194	0.00189
East Asian	0.0000555	0.0000544
Finnish	0.00206	0.00203
European (Non-Finnish)	0.00263	0.00256
Middle Eastern	0.0000555	0.0000544
South Asian	0.00403	0.00389
Other	0.00136	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes phosphoramidate and acyl-adenylate substrates. {ECO:0000269|PubMed:17870088}.

Recessive Scores

• pRec: 0.0778

Intolerance Scores

• loftool: 0.457
• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.72

Haploinsufficiency Scores

• pHI: 0.0442
• hipred: N
• hipred_score: 0.201
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.401

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hint3

Gene ontology

• Cellular component: nucleus;cytoplasm
• Molecular function: nucleotide binding;hydrolase activity