CDK5RAP1

CDK5 regulatory subunit associated protein 1, the group of Radical S-adenosylmethionine domain containing

Basic information

Region (hg38): 20:33358839-33401561

Previous symbols: [ "C20orf34" ]

Links

ENSG00000101391 ∙ NCBI:51654 ∙ OMIM:608200 ∙ HGNC:15880 ∙ Uniprot:Q96SZ6 ∙ 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 CDK5RAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK5RAP1 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			38	1		39
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	38	2	0

Variants in CDK5RAP1

This is a list of pathogenic ClinVar variants found in the CDK5RAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-33360391-A-G		not specified	Uncertain significance (Dec 03, 2021)
20-33360430-A-G		not specified	Uncertain significance (Sep 20, 2023)
20-33366912-T-C		not specified	Uncertain significance (Dec 07, 2024)
20-33366929-A-T		not specified	Uncertain significance (Jan 23, 2023)
20-33366971-G-A		not specified	Uncertain significance (Aug 16, 2021)
20-33367001-C-T		not specified	Uncertain significance (Apr 06, 2024)
20-33370579-C-G		not specified	Uncertain significance (May 01, 2022)
20-33370584-G-A		not specified	Uncertain significance (Jun 29, 2022)
20-33370591-C-G		not specified	Uncertain significance (Mar 19, 2024)
20-33370612-C-T		not specified	Uncertain significance (Jan 31, 2022)
20-33372648-T-C		not specified	Uncertain significance (Aug 28, 2024)
20-33372662-T-C		not specified	Uncertain significance (Sep 26, 2024)
20-33379456-C-T		not specified	Uncertain significance (Jun 18, 2019)
20-33379530-C-G		not specified	Uncertain significance (Apr 06, 2024)
20-33379531-T-C		not specified	Uncertain significance (Jun 12, 2023)
20-33379553-G-A		not specified	Uncertain significance (Jun 05, 2023)
20-33379619-T-C		not specified	Uncertain significance (Oct 05, 2023)
20-33385691-T-C		not specified	Likely benign (Dec 07, 2023)
20-33385697-G-A		not specified	Uncertain significance (Dec 13, 2023)
20-33385715-G-A		not specified	Uncertain significance (Mar 25, 2022)
20-33385738-C-T		not specified	Uncertain significance (Dec 21, 2023)
20-33385762-A-G		not specified	Uncertain significance (May 03, 2023)
20-33385763-T-G		not specified	Uncertain significance (Dec 03, 2021)
20-33387338-G-A		not specified	Uncertain significance (Oct 19, 2024)
20-33387399-C-T		not specified	Uncertain significance (Aug 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDK5RAP1	protein_coding	protein_coding	ENST00000346416	13	42723

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.78e-19	0.00395	125615	0	133	125748	0.000529

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	277	342	0.810	0.0000192	3846
Missense in Polyphen		94	134.45	0.69914		1509
Synonymous	0.364	117	122	0.958	0.00000641	1154
Loss of Function	0.0555	28	28.3	0.989	0.00000137	337

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000605	0.000605
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000708	0.000707
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000758	0.000756
Middle Eastern	0.000708	0.000707
South Asian	0.000557	0.000555
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically inhibits CDK5 activation by CDK5R1.
• 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: 0.124

Intolerance Scores

• loftool: 0.271
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.46

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.407
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdk5rap1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: brain development;tRNA methylthiolation;regulation of neuron differentiation;negative regulation of cyclin-dependent protein serine/threonine kinase activity;positive regulation of translational fidelity;positive regulation of mitochondrial translation;mitochondrial tRNA modification
• Cellular component: cellular_component;mitochondrion
• Molecular function: protein kinase binding;N6-isopentenyladenosine methylthiotransferase activity;protein-containing complex binding;metal ion binding;4 iron, 4 sulfur cluster binding