CDK2AP2

cyclin dependent kinase 2 associated protein 2

Basic information

Region (hg38): 11:67506497-67508649

Links

ENSG00000167797 ∙ NCBI:10263 ∙ OMIM:620061 ∙ HGNC:30833 ∙ Uniprot:O75956 ∙ 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 CDK2AP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK2AP2 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				2		2
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	6	2	0

Variants in CDK2AP2

This is a list of pathogenic ClinVar variants found in the CDK2AP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-67506957-G-A			Likely benign (Jul 10, 2018)
11-67507387-G-T		not specified	Uncertain significance (Oct 01, 2024)
11-67507431-C-G		not specified	Uncertain significance (Apr 05, 2023)
11-67507455-T-C		not specified	Uncertain significance (Jan 24, 2025)
11-67507494-T-G		not specified	Uncertain significance (Apr 17, 2024)
11-67507592-C-T			Benign (Jul 31, 2018)
11-67507596-A-T		not specified	Uncertain significance (Dec 28, 2022)
11-67507599-T-C		not specified	Uncertain significance (Mar 22, 2023)
11-67507605-A-G		not specified	Uncertain significance (May 24, 2023)
11-67507639-T-G			Likely benign (Mar 29, 2018)
11-67508027-G-A		not specified	Uncertain significance (Jan 14, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDK2AP2	protein_coding	protein_coding	ENST00000301488	4	2153

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.788	0.206	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	41	76.2	0.538	0.00000447	781
Missense in Polyphen		9	24.777	0.36324		250
Synonymous	0.166	31	32.2	0.963	0.00000194	271
Loss of Function	2.10	0	5.13	0.00	2.17e-7	67

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: Plays a role in regulating the self-renewal of embryonic stem cells (ESCs) and in maintaining cell survival during terminal differentiation of ESCs. Regulates microtubule organization of metaphase II oocytes (By similarity). Inhibits cell cycle G1/S phase transition by repressing CDK2 expression and activation; represses CDK2 activation by inhibiting its interaction with cyclin E and A (PubMed:23781148). {ECO:0000250|UniProtKB:Q9CPY4, ECO:0000269|PubMed:23781148}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.190
• rvis_EVS: 0.1
• rvis_percentile_EVS: 60.96

Haploinsufficiency Scores

• pHI: 0.478
• hipred: N
• hipred_score: 0.375
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.540

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdk2ap2

Gene ontology

• Biological process: regulation of microtubule cytoskeleton organization;regulation of stem cell division;negative regulation of G1/S transition of mitotic cell cycle
• Cellular component: nucleus;cytoplasm;microtubule
• Molecular function: protein binding