HINT2

protein-coding

histidine triad nucleotide binding protein 2, the group of Histidine triad superfamily

Gene summary

Histidine triad proteins, such as HINT2, 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_032593.3

Inheritance

—

ClinVar variants

U:23B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1

Max pathogenic AF

—

Genomic locus

chr9:35,812,960-35,815,354

External References & Databases

Ensembl (ENSG00000137133)

Transcript & Mutation Effects

hg38 • Region Span ~2.4 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 HINT2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 28

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032593.3. 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			23 clinvar	5 clinvar		28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	5	0	28

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032593.3	RefSeq	NP_115982.1	5	MANE Select
ENST00000259667.6	Ensembl	ENSP00000259667.5	5	MANE Select
ENST00000851670.1	Ensembl	ENSP00000521729.1	5	Standard
ENST00000851671.1	Ensembl	ENSP00000521730.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

steroid biosynthetic process
apoptotic process
lipid catabolic process
negative regulation of peptidyl-lysine acetylation

Molecular Function

nucleotide binding
hydrolase activity

Cellular Component

nucleolus
mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000259667
Coding exons: 5
Length: 2395
Individuals with no LoFs: 125682
Homozygous LoFs: 1
Heterozygous LoFs: 65
Defined: 125748
p: 0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.353	95	85.8	1.11	0.00000459	1018
Missense (PolyPhen)		29	32.035	0.90526		362
Synonymous	0.474	29	32.4	0.894	0.00000154	364
Loss of Function	-0.00585	8	7.98	1.00	4.25e-7	87

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00055	0.00055	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00028	0.00028	rare
South Asian	0.00065	0.00062	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Hydrolase probably involved in steroid biosynthesis. May play a role in apoptosis. Has adenosine phosphoramidase activity. {ECO:0000269|PubMed:16762638, ECO:0000269|PubMed:18653718}.;

Recessive Scores

pRec: 0.0837

Intolerance Scores

LoFtool: 0.631
RVIS EVS: -0.08
RVIS percentile EVS: 47.79

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

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