CDK11A

cyclin dependent kinase 11A, the group of Cyclin dependent kinases

Basic information

Region (hg38): 1:1702378-1724357

Previous symbols: [ "CDC2L3", "CDC2L2" ]

Links

ENSG00000008128 ∙ NCBI:728642 ∙ OMIM:116951 ∙ HGNC:1730 ∙ Uniprot:Q9UQ88 ∙ 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 CDK11A gene.

• Inborn genetic diseases (30 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK11A 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				5		5
missense			30	2		32
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	7	0

Variants in CDK11A

This is a list of pathogenic ClinVar variants found in the CDK11A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-1703487-G-A			Likely benign (Mar 01, 2023)
1-1703489-C-T			Likely benign (Oct 01, 2023)
1-1703490-G-C		not specified	Uncertain significance (Jan 22, 2024)
1-1703515-C-G		not specified	Uncertain significance (Jan 09, 2024)
1-1703521-C-T		not specified	Uncertain significance (Mar 14, 2023)
1-1703522-G-A		not specified	Uncertain significance (Nov 29, 2023)
1-1703528-G-A		not specified	Uncertain significance (Jan 29, 2024)
1-1703608-CT-C			not provided (-)
1-1703882-G-A		not specified	Uncertain significance (Dec 22, 2023)
1-1703917-C-G		not specified	Uncertain significance (Jan 02, 2024)
1-1704062-G-C		not specified	Uncertain significance (Dec 19, 2022)
1-1704065-C-T		not specified	Uncertain significance (Sep 17, 2021)
1-1704068-G-A		not specified	Uncertain significance (May 31, 2023)
1-1704076-T-A			Likely benign (Feb 01, 2023)
1-1704112-G-T		not specified	Uncertain significance (Oct 12, 2022)
1-1704124-C-T		not specified	Uncertain significance (May 24, 2023)
1-1704133-C-T		not specified	Uncertain significance (Feb 07, 2023)
1-1704135-A-G			Likely benign (Nov 01, 2022)
1-1704138-A-G			Likely benign (Nov 01, 2022)
1-1704238-G-A			Likely benign (Jan 01, 2023)
1-1704272-C-T		not specified	Uncertain significance (Jan 25, 2023)
1-1704291-C-T		not specified	Uncertain significance (Apr 29, 2022)
1-1704596-G-T		not specified	Uncertain significance (Jan 31, 2024)
1-1704643-C-T		not specified	Uncertain significance (May 04, 2023)
1-1704651-A-G		not specified	Uncertain significance (Nov 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDK11A	protein_coding	protein_coding	ENST00000404249	19	21598

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.38e-17	0.0112	124054	4	583	124641	0.00236

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.828	339	299	1.13	0.0000188	5028
Missense in Polyphen		54	63.928	0.8447		1211
Synonymous	-3.12	163	120	1.36	0.00000791	1336
Loss of Function	0.316	27	28.8	0.936	0.00000155	525

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00125	0.00125
Ashkenazi Jewish	0.00	0.00
East Asian	0.000224	0.000223
Finnish	0.0123	0.0121
European (Non-Finnish)	0.00197	0.00189
Middle Eastern	0.000224	0.000223
South Asian	0.00206	0.00196
Other	0.00291	0.00281

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Appears to play multiple roles in cell cycle progression, cytokinesis and apoptosis. The p110 isoforms have been suggested to be involved in pre-mRNA splicing, potentially by phosphorylating the splicing protein SFRS7. The p58 isoform may act as a negative regulator of normal cell cycle progression. {ECO:0000269|PubMed:12501247, ECO:0000269|PubMed:12624090}.
• Pathway: terminal <i>O</i>-glycans residues modification;Recruitment of mitotic centrosome proteins and complexes;Centrosome maturation;G2/M Transition;Mitotic G2-G2/M phases;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.141

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.370
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: mitotic cell cycle;regulation of cell growth;regulation of transcription, DNA-templated;protein phosphorylation;apoptotic process;regulation of mRNA processing;regulation of cell cycle
• Cellular component: nucleus;cytoplasm
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;cyclin-dependent protein serine/threonine kinase activity;ATP binding