CCNT2

cyclin T2, the group of Cyclins|P-TEFb complex subunits

Basic information

Region (hg38): 2:134918235-134959342

Links

ENSG00000082258 ∙ NCBI:905 ∙ OMIM:603862 ∙ HGNC:1600 ∙ Uniprot:O60583 ∙ 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 CCNT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCNT2 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	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in CCNT2

This is a list of pathogenic ClinVar variants found in the CCNT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-134918961-G-A		not specified	Likely benign (Sep 22, 2023)
2-134919875-C-G		not specified	Uncertain significance (Dec 21, 2022)
2-134939047-A-G		not specified	Uncertain significance (Jul 05, 2023)
2-134939063-G-C		Premature ovarian insufficiency	Uncertain significance (Jan 10, 2018)
2-134953258-T-C		not specified	Uncertain significance (Mar 29, 2024)
2-134953299-T-G		not specified	Uncertain significance (Mar 29, 2023)
2-134953424-A-C		not specified	Uncertain significance (Jan 03, 2024)
2-134953434-A-G		not specified	Uncertain significance (Dec 21, 2022)
2-134953533-A-G		not specified	Uncertain significance (Mar 11, 2024)
2-134953549-C-T		not specified	Uncertain significance (Jan 31, 2022)
2-134953590-A-G		not specified	Uncertain significance (Apr 19, 2023)
2-134953606-G-A		not specified	Uncertain significance (Jan 03, 2022)
2-134953635-C-T		not specified	Uncertain significance (Jan 23, 2024)
2-134953731-A-G		not specified	Uncertain significance (Sep 01, 2021)
2-134953759-C-T		not specified	Uncertain significance (Jan 30, 2024)
2-134953827-G-A		not specified	Uncertain significance (Apr 05, 2023)
2-134953986-A-G		not specified	Uncertain significance (Sep 17, 2021)
2-134954151-A-G		not specified	Uncertain significance (Mar 23, 2023)
2-134954232-G-A		not specified	Uncertain significance (Nov 22, 2021)
2-134954239-C-T		not specified	Uncertain significance (May 10, 2024)
2-134954247-G-A		not specified	Uncertain significance (Dec 28, 2022)
2-134954281-G-A		not specified	Uncertain significance (Oct 27, 2022)
2-134954428-A-T		not specified	Uncertain significance (Feb 27, 2023)
2-134954446-A-T		not specified	Uncertain significance (Mar 30, 2024)
2-134954517-G-T		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCNT2	protein_coding	protein_coding	ENST00000264157	9	41108

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.927	0.0732	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.77	292	391	0.748	0.0000188	4821
Missense in Polyphen		103	172.57	0.59685		2161
Synonymous	-0.402	151	145	1.04	0.00000763	1390
Loss of Function	4.27	5	30.4	0.165	0.00000143	382

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000471	0.0000462
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000109	0.000109
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 T) complex, also called positive transcription elongation factor B (P-TEFB), which is proposed to facilitate the transition from abortive to production elongation by phosphorylating the CTD (carboxy-terminal domain) of the large subunit of RNA polymerase II (RNAP II) (PubMed:9499409, PubMed:15563843). The activity of this complex is regulated by binding with 7SK snRNA (PubMed:11713533). Plays a role during muscle differentiation; P-TEFB complex interacts with MYOD1; this tripartite complex promotes the transcriptional activity of MYOD1 through its CDK9-mediated phosphorylation and binds the chromatin of promoters and enhancers of muscle-specific genes; this event correlates with hyperphosphorylation of the CTD domain of RNA pol II (By similarity). In addition, enhances MYOD1-dependent transcription through interaction with PKN1 (PubMed:16331689). Involved in early embryo development (By similarity). {ECO:0000250|UniProtKB:Q7TQK0, ECO:0000269|PubMed:11713533, ECO:0000269|PubMed:15563843, ECO:0000269|PubMed:16331689, ECO:0000269|PubMed:9499409}.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Disease;Signal Transduction;Gene expression (Transcription);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;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;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;Transcriptional Regulation by TP53;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.655
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.3

Haploinsufficiency Scores

• pHI: 0.934
• hipred: Y
• hipred_score: 0.745
• ghis: 0.694

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccnt2
• Phenotype: 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: 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;skeletal muscle tissue development;early viral transcription;late viral transcription;positive regulation of DNA-templated transcription, elongation;snRNA transcription by RNA polymerase II;positive regulation of cyclin-dependent protein serine/threonine kinase activity;positive regulation of transcription by RNA polymerase II;cell division
• Cellular component: nucleus;nucleoplasm;cytosol;plasma membrane;cyclin/CDK positive transcription elongation factor complex;perinuclear region of cytoplasm
• Molecular function: transcription coactivator binding;chromatin binding;protein serine/threonine kinase activity;protein binding;cyclin-dependent protein serine/threonine kinase regulator activity;cyclin-dependent protein serine/threonine kinase activator activity;RNA polymerase binding;7SK snRNA binding