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

ENSG00000101391NCBI:51654OMIM:608200HGNC:15880Uniprot:Q96SZ6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDK5RAP1 gene.

  • not_specified (63 variants)
  • not_provided (1 variants)

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. These statistics are base on transcript: NM_000016408.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
60
clinvar
2
clinvar
62
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 60 3 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CDK5RAP1protein_codingprotein_codingENST00000346416 1342723
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
7.78e-190.0039512561501331257480.000529
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.252773420.8100.00001923846
Missense in Polyphen94134.450.699141509
Synonymous0.3641171220.9580.000006411154
Loss of Function0.05552828.30.9890.00000137337

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006050.000605
Ashkenazi Jewish0.0001010.0000992
East Asian0.0007080.000707
Finnish0.00009240.0000924
European (Non-Finnish)0.0007580.000756
Middle Eastern0.0007080.000707
South Asian0.0005570.000555
Other0.0001670.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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