HINT3

protein-coding

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

Gene summary

Histidine triad proteins, such as HINT3, are nucleotide hydrolases and transferases that act on the alpha-phosphate of ribonucleotides (Brenner, 2002 [PubMed 12119013]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_138571.5

Inheritance

—

ClinVar variants

U:27

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.08

Max pathogenic AF

—

Genomic locus

chr6:125,956,770-125,980,244

External References & Databases

Ensembl (ENSG00000111911)

Transcript & Mutation Effects

hg38 • Region Span ~23.5 kb

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GenCC 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 HINT3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 26

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138571.5. 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			26 clinvar			26
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	27	0	0	27

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138571.5	RefSeq	NP_612638.3	5	MANE Select
ENST00000229633.7	Ensembl	ENSP00000229633.5	5	MANE Select
ENST00000855676.1	Ensembl	ENSP00000525735.1	5	Standard
ENST00000855676.2	Ensembl	ENSP00000525735.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

nucleotide binding
hydrolase activity

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000229633
Coding exons: 5
Length: 23461
Individuals with no LoFs: 125227
Homozygous LoFs: 2
Heterozygous LoFs: 507
Defined: 125736
p: 0.00203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.594	82	98.6	0.832	0.00000434	1189
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00072	0.00067	rare
Ashkenazi Jewish	0.0019	0.0019	notable
East Asian	0.000055	0.000054	rare
Finnish	0.0021	0.0020	notable
European (Non-Finnish)	0.0026	0.0026	notable
South Asian	0.0040	0.0039	notable
Other	0.0014	0.0013	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.401

Gene Damage Prediction

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