HTATIP2

protein-coding

HIV-1 Tat interactive protein 2, the group of Short chain dehydrogenase/reductase superfamily

Gene summary

Enables protein serine/threonine kinase activity. Acts upstream of or within positive regulation of programmed cell death; positive regulation of transcription by RNA polymerase II; and protein autophosphorylation. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001098522.2

Inheritance

—

ClinVar variants

U:40

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.43

Max pathogenic AF

—

Genomic locus

chr11:20,363,685-20,383,782

External References & Databases

Ensembl (ENSG00000109854)

Transcript & Mutation Effects

hg38 • Region Span ~20.1 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 HTATIP2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 37

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001098522.2. 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			39 clinvar			39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	40	0	0	40

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001098522.2	RefSeq	NP_001091992.1	5	MANE Select
ENST00000451739.7	Ensembl	ENSP00000394259.2	5	MANE Select
NM_001098520.2	RefSeq	NP_001091990.1	6	Standard
NM_001098521.2	RefSeq	NP_001091991.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

angiogenesis
regulation of transcription by RNA polymerase II
apoptotic process
viral process
cell differentiation

Molecular Function

transcription coactivator activity
protein binding
oxidoreductase activity

Cellular Component

nucleus
nuclear envelope
cytoplasm
cytosol
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000419348
Coding exons: 6
Length: 20099
Individuals with no LoFs: 125662
Homozygous LoFs: 0
Heterozygous LoFs: 86
Defined: 125748
p: 0.000342

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.547	121	139	0.870	0.00000720	1769
Missense (PolyPhen)		47	49.704	0.94559		546
Synonymous	0.123	55	56.2	0.979	0.00000298	567
Loss of Function	-1.32	16	11.2	1.43	5.56e-7	146

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00047	0.00046	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00082	0.00082	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00030	0.00030	rare
South Asian	0.00023	0.00023	rare
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Oxidoreductase required for tumor suppression. NAPDH- bound form inhibits nuclear import by competing with nuclear import substrates for binding to a subset of nuclear transport receptors. May act as a redox sensor linked to transcription through regulation of nuclear import. Isoform 1 is a metastasis suppressor with proapoptotic as well as antiangiogenic properties. Isoform 2 has an antiapoptotic effect. {ECO:0000269|PubMed:10611237, ECO:0000269|PubMed:11313954, ECO:0000269|PubMed:15282309, ECO:0000269|PubMed:9174052}.;

Recessive Scores

pRec: 0.176

Intolerance Scores

LoFtool: 0.994
RVIS EVS: -0.16
RVIS percentile EVS: 41.64

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.420

Gene Damage Prediction

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