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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 2 of 2.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_006460.3	NP_006451.1	1	yes	-
ENST00000332499.4	ENSP00000328773.3	1	yes	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HEXIM1 gene.

• not_specified (38 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_006460.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			37	1		38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	37	1	1

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	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

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

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