CDK5RAP3

CDK5 regulatory subunit associated protein 3

Basic information

Region (hg38): 17:47967810-47981781

Links

ENSG00000108465 ∙ NCBI:80279 ∙ OMIM:608202 ∙ HGNC:18673 ∙ Uniprot:Q96JB5 ∙ 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 CDK5RAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK5RAP3 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			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	2	0

Variants in CDK5RAP3

This is a list of pathogenic ClinVar variants found in the CDK5RAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-47973608-A-G		not specified	Uncertain significance (Apr 26, 2023)
17-47973611-C-A		not specified	Uncertain significance (Nov 10, 2024)
17-47973629-G-A		not specified	Uncertain significance (Nov 09, 2024)
17-47973973-A-G		not specified	Uncertain significance (Feb 21, 2024)
17-47973991-C-T		not specified	Uncertain significance (Dec 03, 2024)
17-47974018-C-T		not specified	Uncertain significance (May 30, 2023)
17-47975203-C-G		not specified	Uncertain significance (Dec 03, 2024)
17-47975203-C-T		not specified	Uncertain significance (Jul 12, 2022)
17-47975297-G-A		not specified	Uncertain significance (Aug 14, 2024)
17-47975521-A-G		not specified	Uncertain significance (Aug 30, 2022)
17-47975560-C-T		not specified	Uncertain significance (Jul 07, 2022)
17-47975562-A-C		not specified	Uncertain significance (Sep 16, 2021)
17-47975587-C-T		not specified	Uncertain significance (Nov 08, 2024)
17-47975590-C-T		not specified	Uncertain significance (Nov 24, 2024)
17-47975888-C-G		not specified	Uncertain significance (Oct 20, 2024)
17-47975889-C-A		not specified	Uncertain significance (Aug 20, 2024)
17-47975903-G-A		not specified	Uncertain significance (Dec 08, 2023)
17-47975918-A-G		not specified	Uncertain significance (Mar 20, 2024)
17-47975933-G-A		not specified	Uncertain significance (Dec 22, 2023)
17-47975957-T-C		not specified	Uncertain significance (Jan 22, 2024)
17-47975970-G-C		not specified	Uncertain significance (Oct 05, 2023)
17-47975981-G-C		not specified	Uncertain significance (Dec 17, 2021)
17-47976012-C-T		not specified	Uncertain significance (Mar 22, 2023)
17-47976741-A-C			Likely benign (Mar 01, 2023)
17-47976743-T-C		not specified	Likely benign (Feb 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDK5RAP3	protein_coding	protein_coding	ENST00000338399	14	13965

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.63e-15	0.217	124720	0	93	124813	0.000373

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.484	258	281	0.919	0.0000155	3262
Missense in Polyphen		79	92.162	0.85718		1169
Synonymous	-0.453	124	118	1.05	0.00000686	989
Loss of Function	1.18	26	33.4	0.779	0.00000178	353

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000449	0.000449
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000514	0.000512
Middle Eastern	0.0000556	0.0000556
South Asian	0.000524	0.000523
Other	0.000826	0.000824

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable tumor suppressor initially identified as a CDK5R1 interactor controlling cell proliferation (PubMed:12054757, PubMed:12737517). Negatively regulates NF-kappa-B-mediated gene transcription through the control of RELA phosphorylation (PubMed:17785205, PubMed:20228063). Also regulates mitotic G2/M transition checkpoint and mitotic G2 DNA damage checkpoint (PubMed:15790566, PubMed:19223857). Through its interaction with CDKN2A/ARF and MDM2 may induce MDM2-dependent p53/TP53 ubiquitination, stabilization and activation in the nucleus, thereby promoting G1 cell cycle arrest and inhibition of cell proliferation (PubMed:16173922). May play a role in the unfolded protein response, mediating the ufmylation of multiple proteins in response to endoplasmic reticulum stress (PubMed:23152784). May also play a role in the rupture of the nuclear envelope during apoptosis (PubMed:23478299). May regulate MAPK14 activity by regulating its dephosphorylation by PPM1D/WIP1 (PubMed:21283629). {ECO:0000269|PubMed:12054757, ECO:0000269|PubMed:12737517, ECO:0000269|PubMed:15790566, ECO:0000269|PubMed:16173922, ECO:0000269|PubMed:17785205, ECO:0000269|PubMed:19223857, ECO:0000269|PubMed:20228063, ECO:0000269|PubMed:21283629, ECO:0000269|PubMed:23152784, ECO:0000269|PubMed:23478299}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.821
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.47

Haploinsufficiency Scores

• pHI: 0.227
• hipred: Y
• hipred_score: 0.575
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.941

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdk5rap3
• 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)

Zebrafish Information Network

• Gene name: cdk5rap3
• Affected structure: blastoderm cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity;negative regulation of protein phosphorylation;mitotic G2 DNA damage checkpoint;regulation of mitotic cell cycle;brain development;cell population proliferation;regulation of phosphatase activity;apoptotic nuclear changes;endoplasmic reticulum unfolded protein response;positive regulation of protein ubiquitination;negative regulation of NF-kappaB transcription factor activity;negative regulation of MAP kinase activity;negative regulation of protein kinase activity by regulation of protein phosphorylation;mitotic G2/M transition checkpoint;regulation of neuron differentiation;positive regulation of transcription by RNA polymerase II;protein ufmylation;negative regulation of protein serine/threonine kinase activity;positive regulation of protein localization to nucleus;positive regulation of signal transduction by p53 class mediator;negative regulation of cellular protein catabolic process;positive regulation of ubiquitin-dependent protein catabolic process
• Cellular component: nucleus;nucleolus;cytoplasm;centrosome;cytosol;microtubule;membrane;protein-containing complex
• Molecular function: protein binding;protein kinase binding;cyclin binding;ubiquitin-like protein ligase binding;mitogen-activated protein kinase binding;NF-kappaB binding;MDM2/MDM4 family protein binding