CDKN3

cyclin dependent kinase inhibitor 3, the group of CDC14 phosphatases

Basic information

Region (hg38): 14:54396849-54420218

Links

ENSG00000100526

∙ NCBI:1033 ∙ OMIM:123832 ∙ HGNC:1791 ∙ Uniprot:Q16667 ∙ 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 CDKN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDKN3 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			3 clinvar			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in CDKN3

This is a list of pathogenic ClinVar variants found in the CDKN3 region.

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

Position	Phenotype	Significance	ClinVar
14-54399905-A-G	not specified	Uncertain significance (Feb 07, 2023)	2480661
14-54411563-C-G	not specified	Uncertain significance (Dec 04, 2024)	3489702
14-54411661-A-G	not specified	Uncertain significance (Feb 28, 2023)	2465430
14-54417934-G-A	not specified	Uncertain significance (Jan 03, 2024)	3141674
14-54420016-C-T	not specified	Uncertain significance (Sep 11, 2024)	3489703

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDKN3	protein_coding	protein_coding	ENST00000335183	8	23370

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00195	0.978	125733	0	11	125744	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	74	109	0.680	0.00000514	1342
Missense in Polyphen		14	35.259	0.39707		413
Synonymous	1.14	29	37.9	0.764	0.00000184	394
Loss of Function	2.05	7	15.8	0.443	9.35e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000594	0.0000544
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.0000542	0.0000527
Middle Eastern	0.0000594	0.0000544
South Asian	0.0000754	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: May play a role in cell cycle regulation. Dual specificity phosphatase active toward substrates containing either phosphotyrosine or phosphoserine residues. Dephosphorylates CDK2 at 'Thr-160' in a cyclin-dependent manner. {ECO:0000269|PubMed:7569954, ECO:0000269|PubMed:8127873, ECO:0000269|PubMed:8242750}.;
Disease: DISEASE: Hepatocellular carcinoma (HCC) [MIM:114550]: A primary malignant neoplasm of epithelial liver cells. The major risk factors for HCC are chronic hepatitis B virus (HBV) infection, chronic hepatitis C virus (HCV) infection, prolonged dietary aflatoxin exposure, alcoholic cirrhosis, and cirrhosis due to other causes. {ECO:0000269|PubMed:10987270}. Note=The gene represented in this entry may be involved in disease pathogenesis.;

Recessive Scores

pRec: 0.135

Intolerance Scores

loftool: 0.812
rvis_EVS: -0.19
rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

pHI: 0.586
hipred: Y
hipred_score: 0.733
ghis: 0.661

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: H
gene_indispensability_pred: E
gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cdkn3
Phenotype

Gene ontology

Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity;G1/S transition of mitotic cell cycle;cell cycle arrest;negative regulation of cell population proliferation;peptidyl-tyrosine dephosphorylation
Cellular component: cytoplasm;cytosol;perinuclear region of cytoplasm
Molecular function: protein serine/threonine phosphatase activity;protein tyrosine phosphatase activity;protein binding;protein tyrosine/serine/threonine phosphatase activity