CCNT1

cyclin T1, the group of P-TEFb complex subunits|Cyclins

Basic information

Region (hg38): 12:48688458-48716998

Previous symbols: [ "HIVE1" ]

Links

ENSG00000129315 ∙ NCBI:904 ∙ OMIM:143055 ∙ HGNC:1599 ∙ Uniprot:O60563 ∙ 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 CCNT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCNT1 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			40	1		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	2	0

Variants in CCNT1

This is a list of pathogenic ClinVar variants found in the CCNT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-48693089-G-A		not specified	Uncertain significance (Nov 26, 2024)
12-48693178-G-C		not specified	Uncertain significance (Jan 07, 2025)
12-48693220-T-G		not specified	Uncertain significance (Mar 02, 2023)
12-48693316-C-T		not specified	Uncertain significance (Jun 29, 2023)
12-48693325-C-T		not specified	Uncertain significance (Dec 15, 2022)
12-48693367-T-C		not specified	Uncertain significance (Oct 10, 2023)
12-48693375-C-A		not specified	Uncertain significance (Oct 12, 2022)
12-48693470-C-G		not specified	Uncertain significance (Oct 04, 2024)
12-48693523-G-A		not specified	Uncertain significance (Jan 09, 2024)
12-48693559-C-T		not specified	Uncertain significance (Oct 20, 2021)
12-48693571-C-T		not specified	Uncertain significance (Jan 22, 2025)
12-48693587-C-T		not specified	Uncertain significance (Jan 16, 2025)
12-48693618-T-A		not specified	Uncertain significance (Mar 15, 2024)
12-48693691-T-A		not specified	Uncertain significance (Mar 28, 2024)
12-48693719-T-C		not specified	Uncertain significance (May 23, 2024)
12-48693733-T-C		not specified	Uncertain significance (Apr 09, 2024)
12-48693734-T-C		not specified	Uncertain significance (Apr 20, 2024)
12-48693766-C-A		not specified	Uncertain significance (Oct 05, 2023)
12-48693767-G-A		not specified	Uncertain significance (Aug 04, 2021)
12-48693784-G-A		not specified	Uncertain significance (Nov 08, 2022)
12-48693805-T-C		not specified	Uncertain significance (Dec 15, 2022)
12-48693826-C-T		not specified	Uncertain significance (Feb 18, 2025)
12-48693858-C-T			Likely benign (Nov 01, 2023)
12-48693869-G-A		not specified	Uncertain significance (Jun 07, 2024)
12-48693889-T-A		not specified	Uncertain significance (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCNT1	protein_coding	protein_coding	ENST00000261900	9	28435

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0511	0.949	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	333	393	0.847	0.0000205	4768
Missense in Polyphen		73	108.01	0.67585		1305
Synonymous	-0.277	144	140	1.03	0.00000712	1431
Loss of Function	3.62	8	29.0	0.276	0.00000140	360

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000141	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin-T1) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to productive elongation by phosphorylating the CTD (carboxy-terminal domain) of the large subunit of RNA polymerase II (RNA Pol II). {ECO:0000269|PubMed:16109376, ECO:0000269|PubMed:16109377}.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Initiation of transcription and translation elongation at the HIV-1 LTR;Disease;Signal Transduction;Gene expression (Transcription);Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;HIV Transcription Elongation;HIV elongation arrest and recovery;Formation of HIV elongation complex in the absence of HIV Tat;Pausing and recovery of HIV elongation;Generic Transcription Pathway;Tat-mediated HIV elongation arrest and recovery;Pausing and recovery of Tat-mediated HIV elongation;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;Interactions of Tat with host cellular proteins;Host Interactions of HIV factors;HIV Infection;RNA Polymerase II Pre-transcription Events;Formation of RNA Pol II elongation complex ;RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;Infectious disease;RNA Polymerase II Transcription Elongation;SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription;Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer;TP53 Regulates Transcription of DNA Repair Genes;Signaling by Nuclear Receptors;Transcriptional Regulation by TP53;Estrogen-dependent gene expression;TNFalpha;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;ESR-mediated signaling (Consensus)

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.314
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.09

Haploinsufficiency Scores

• pHI: 0.603
• hipred: Y
• hipred_score: 0.783
• ghis: 0.545

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccnt1

Gene ontology

• Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;protein phosphorylation;cell cycle;viral process;positive regulation of DNA-templated transcription, elongation;snRNA transcription by RNA polymerase II;positive regulation by host of viral transcription;positive regulation of cyclin-dependent protein serine/threonine kinase activity;positive regulation of transcription by RNA polymerase II;positive regulation of viral transcription;cell division;negative regulation of mRNA polyadenylation
• Cellular component: nucleus;nucleoplasm;nucleolus;cyclin/CDK positive transcription elongation factor complex
• Molecular function: DNA binding;chromatin binding;protein serine/threonine kinase activity;protein binding;transcription factor binding;cyclin-dependent protein serine/threonine kinase regulator activity;protein kinase binding;transcription regulatory region DNA binding;cyclin-dependent protein serine/threonine kinase activator activity;RNA polymerase binding;7SK snRNA binding