HINT2

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

Basic information

Region (hg38): 9:35812960-35815354

Links

ENSG00000137133 ∙ NCBI:84681 ∙ OMIM:609997 ∙ HGNC:18344 ∙ Uniprot:Q9BX68 ∙ 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 HINT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HINT2 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			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in HINT2

This is a list of pathogenic ClinVar variants found in the HINT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-35813080-G-A		not specified	Uncertain significance (Oct 04, 2024)
9-35813080-G-C		not specified	Uncertain significance (Oct 16, 2024)
9-35813082-C-A		not specified	Uncertain significance (Dec 03, 2024)
9-35813139-T-C		not specified	Uncertain significance (Apr 12, 2023)
9-35813280-T-A		not specified	Uncertain significance (Oct 03, 2024)
9-35813454-T-G		not specified	Likely benign (Sep 25, 2023)
9-35813462-C-T		not specified	Uncertain significance (Mar 14, 2023)
9-35813464-G-T		not specified	Uncertain significance (Apr 26, 2024)
9-35813476-C-T		not specified	Uncertain significance (May 08, 2024)
9-35813524-G-A		not specified	Uncertain significance (Apr 22, 2024)
9-35813693-C-T		not specified	Uncertain significance (Jan 23, 2023)
9-35813700-A-T		not specified	Uncertain significance (Oct 17, 2023)
9-35813762-G-A		not specified	Uncertain significance (Apr 07, 2023)
9-35814907-C-T		not specified	Uncertain significance (Jun 06, 2023)
9-35814963-A-C		not specified	Uncertain significance (Dec 03, 2024)
9-35814969-G-A		not specified	Likely benign (Feb 06, 2023)
9-35814969-G-C		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HINT2	protein_coding	protein_coding	ENST00000259667	5	2395

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000535	0.259	125682	1	65	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.353	95	85.8	1.11	0.00000459	1018
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000612	0.000612
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000281	0.000281
Middle Eastern	0.000163	0.000163
South Asian	0.000653	0.000621
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0975
• hipred: N
• hipred_score: 0.167
• ghis: 0.438

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hint2
• Phenotype: liver/biliary system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: steroid biosynthetic process;apoptotic process;lipid catabolic process;negative regulation of peptidyl-lysine acetylation
• Cellular component: nucleolus;mitochondrion
• Molecular function: nucleotide binding;hydrolase activity