HTATIP2

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

Basic information

Region (hg38): 11:20363685-20383782

Links

ENSG00000109854 ∙ NCBI:10553 ∙ OMIM:605628 ∙ HGNC:16637 ∙ Uniprot:Q9BUP3 ∙ 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 HTATIP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTATIP2 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1		2
Total	0	0	24	1	0

Variants in HTATIP2

This is a list of pathogenic ClinVar variants found in the HTATIP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-20363827-G-T		not specified	Uncertain significance (Nov 08, 2024)
11-20363846-C-T		not specified	Likely benign (Aug 15, 2023)
11-20364251-A-G		not specified	Uncertain significance (Jul 05, 2024)
11-20364253-G-A		not specified	Uncertain significance (Oct 27, 2023)
11-20364292-A-G		not specified	Uncertain significance (Dec 21, 2023)
11-20364308-T-G		not specified	Uncertain significance (Feb 21, 2024)
11-20364328-G-C		not specified	Uncertain significance (May 26, 2024)
11-20364385-A-G		not specified	Uncertain significance (Oct 05, 2023)
11-20364386-T-C		not specified	Uncertain significance (Jan 19, 2024)
11-20364392-G-A		not specified	Uncertain significance (Apr 25, 2022)
11-20364396-G-C		not specified	Uncertain significance (May 13, 2024)
11-20364422-A-C		not specified	Uncertain significance (May 04, 2023)
11-20367231-C-T		not specified	Uncertain significance (Jun 19, 2024)
11-20367243-T-G		not specified	Uncertain significance (Nov 20, 2024)
11-20367280-C-T		not specified	Uncertain significance (Nov 10, 2024)
11-20376631-G-A		not specified	Uncertain significance (Oct 08, 2024)
11-20376659-A-G		not specified	Uncertain significance (Apr 29, 2024)
11-20382178-G-A		not specified	Uncertain significance (Nov 15, 2024)
11-20382184-G-A		not specified	Uncertain significance (May 03, 2023)
11-20382190-G-A		not specified	Uncertain significance (Dec 15, 2022)
11-20382235-C-T		not specified	Uncertain significance (Oct 06, 2022)
11-20382989-A-T		not specified	Uncertain significance (Jun 05, 2024)
11-20383077-G-A		not specified	Uncertain significance (Oct 24, 2024)
11-20383092-G-A		not specified	Uncertain significance (Oct 17, 2024)
11-20383113-A-C		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTATIP2	protein_coding	protein_coding	ENST00000419348	6	20099

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.38e-13	0.00417	125662	0	86	125748	0.000342

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.547	121	139	0.870	0.00000720	1769
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000721	0.000721
Ashkenazi Jewish	0.000110	0.0000992
East Asian	0.000817	0.000816
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000302	0.000299
Middle Eastern	0.000817	0.000816
South Asian	0.000230	0.000229
Other	0.00132	0.00130

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.197
• hipred: N
• hipred_score: 0.197
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.420

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Htatip2
• Phenotype: neoplasm; cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype

Gene ontology

• Biological process: angiogenesis;regulation of transcription by RNA polymerase II;apoptotic process;viral process;cell differentiation;negative regulation of apoptotic process;regulation of angiogenesis;import into nucleus;oxidation-reduction process;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleus;nuclear envelope;cytoplasm;cytosol;membrane
• Molecular function: transcription coactivator activity;protein binding;oxidoreductase activity