HEXIM1

HEXIM P-TEFb complex subunit 1, the group of P-TEFb complex subunits

Basic information

Region (hg38): 17:45148475-45152099

Links

ENSG00000186834 ∙ NCBI:10614 ∙ OMIM:607328 ∙ HGNC:24953 ∙ Uniprot:O94992 ∙ 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 HEXIM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HEXIM1 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					1	1
missense			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	1

Variants in HEXIM1

This is a list of pathogenic ClinVar variants found in the HEXIM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-45149203-T-C		not specified	Likely benign (Feb 21, 2024)
17-45149231-A-G		not specified	Uncertain significance (Feb 10, 2025)
17-45149290-C-G		not specified	Uncertain significance (Jan 22, 2024)
17-45149298-G-C			Benign (Jul 17, 2018)
17-45149302-G-A		not specified	Uncertain significance (Sep 14, 2023)
17-45149356-G-C		not specified	Uncertain significance (Jan 23, 2023)
17-45149363-G-A		not specified	Uncertain significance (Jan 10, 2022)
17-45149363-G-T		not specified	Uncertain significance (Oct 29, 2021)
17-45149384-G-A		not specified	Uncertain significance (May 14, 2024)
17-45149429-C-A		not specified	Uncertain significance (Jan 08, 2024)
17-45149439-C-G		not specified	Uncertain significance (Feb 22, 2025)
17-45149479-T-G		not specified	Uncertain significance (Mar 01, 2024)
17-45149488-G-A		not specified	Uncertain significance (May 22, 2023)
17-45149558-A-C		not specified	Uncertain significance (Apr 15, 2024)
17-45149564-C-T		not specified	Uncertain significance (Apr 19, 2023)
17-45149692-T-C		not specified	Uncertain significance (Jan 25, 2023)
17-45149723-T-G		not specified	Uncertain significance (Mar 30, 2024)
17-45149746-G-T		not specified	Uncertain significance (Nov 14, 2023)
17-45149926-G-C		not specified	Uncertain significance (Jul 30, 2024)
17-45150134-T-C		not specified	Uncertain significance (Dec 31, 2024)
17-45150224-T-G		not specified	Uncertain significance (Oct 28, 2024)
17-45150230-G-A		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HEXIM1	protein_coding	protein_coding	ENST00000332499	1	4785

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.984	0.0160	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	141	197	0.717	0.00000946	2339
Missense in Polyphen		27	65.849	0.41003		820
Synonymous	-1.88	111	88.5	1.25	0.00000453	708
Loss of Function	3.28	0	12.6	0.00	5.54e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional regulator which functions as a general RNA polymerase II transcription inhibitor (PubMed:14580347, PubMed:15713661, PubMed:15201869). In cooperation with 7SK snRNA sequesters P-TEFb in a large inactive 7SK snRNP complex preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation (PubMed:12832472, PubMed:14580347, PubMed:15713661, PubMed:15201869). May also regulate NF-kappa-B, ESR1, NR3C1 and CIITA-dependent transcriptional activity (PubMed:15940264, PubMed:15941832, PubMed:17088550). Plays a role in the regulation of DNA virus-mediated innate immune response by assembling into the HDP-RNP complex, a complex that serves as a platform for IRF3 phosphorylation and subsequent innate immune response activation through the cGAS-STING pathway (PubMed:28712728). {ECO:0000269|PubMed:12581153, ECO:0000269|PubMed:12832472, ECO:0000269|PubMed:14580347, ECO:0000269|PubMed:15201869, ECO:0000269|PubMed:15713661, ECO:0000269|PubMed:15940264, ECO:0000269|PubMed:15941832, ECO:0000269|PubMed:17088550, ECO:0000269|PubMed:28712728}.
• Pathway: Initiation of transcription and translation elongation at the HIV-1 LTR (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.115
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.0922
• hipred: Y
• hipred_score: 0.775
• ghis: 0.519

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.966

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hexim1
• Phenotype: muscle phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;activation of innate immune response;heart development;innate immune response;negative regulation of cyclin-dependent protein serine/threonine kinase activity;negative regulation of transcription, DNA-templated;positive regulation of signal transduction by p53 class mediator
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: cyclin-dependent protein serine/threonine kinase inhibitor activity;protein binding;snRNA binding;7SK snRNA binding