GeneBe

CDC5L

protein-coding

cell division cycle 5 like, the group of NineTeen complex|Spliceosomal C complex|Myb/SANT domain containing|MicroRNA protein coding host genes

Gene summary

The protein encoded by this gene shares a significant similarity with Schizosaccharomyces pombe cdc5 gene product, which is a cell cycle regulator important for G2/M transition. This protein has been demonstrated to act as a positive regulator of cell cycle G2/M progression. It was also found to be an essential component of a non-snRNA spliceosome, which contains at least five additional protein factors and is required for the second catalytic step of pre-mRNA splicing. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001253.4

Inheritance

—

ClinVar variants

U:80B:19

Top phenotype

CDC5L-related disorder

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chr6:44,387,706-44,450,425

External References & Databases

Ensembl (ENSG00000096401)NCBI Gene (988)OMIM (602868)HGNC:1743GenCCUniProt (Q99459)AlphaFoldClinVar (CDC5L)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~62.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CDC5L variants in ClinVar

4 Conditions Cataloged
not specifiedTotal: 69
CDC5L-related disorderTotal: 20
not providedTotal: 10
Congenital anomaly of kidney and urinary tractTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001253.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
4
clinvar
12
clinvar
3
clinvar
 19
missense
71
clinvar
3
clinvar
1
clinvar
 75
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
4
clinvar
 4
Total008015499
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001253.4RefSeqNP_001244.116MANE Select
ENST00000371477.4EnsemblENSP00000360532.316MANE Select
ENST00000862194.1EnsemblENSP00000532253.115Standard
ENST00000862194.2EnsemblENSP00000532253.115Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Spliceosome - Homo sapiens (human)
  • Metabolism of RNA
  • mRNA Splicing - Major Pathway
  • mRNA Splicing
  • Processing of Capped Intron-Containing Pre-mRNA

Biological Process

  • mitotic cell cycle
  • mRNA splicing, via spliceosome
  • DNA repair
  • cellular response to fibroblast growth factor stimulus
  • positive regulation of transcription by RNA polymerase II

Molecular Function

  • RNA polymerase II regulatory region sequence-specific DNA binding
  • DNA-binding transcription factor activity, RNA polymerase II-specific
  • transcription corepressor binding
  • DNA-binding transcription activator activity, RNA polymerase II-specific
  • DNA binding

Cellular Component

  • Prp19 complex
  • nucleus
  • nucleoplasm
  • DNA replication factor A complex
  • cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000371477
Coding exons
16
Length
62902
Individuals with no LoFs
125697
Homozygous LoFs
0
Heterozygous LoFs
6
Defined
125703
p
0.0000239
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.782684300.6230.00002275267
Missense (PolyPhen)32126.880.252211543
Synonymous-0.7291581471.080.000007521487
Loss of Function6.21248.80.04100.00000302548

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.000120.00012rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.0000460.000046rare
European (Non-Finnish)0.00000890.0000088rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: DNA-binding protein involved in cell cycle control. May act as a transcription activator. Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing. The PRP19-CDC5L complex may also play a role in the response to DNA damage (DDR). {ECO:0000269|PubMed:10570151, ECO:0000269|PubMed:11082045, ECO:0000269|PubMed:11101529, ECO:0000269|PubMed:11544257, ECO:0000269|PubMed:12927788, ECO:0000269|PubMed:18583928, ECO:0000269|PubMed:24332808, ECO:0000269|PubMed:9038199, ECO:0000269|PubMed:9468527, ECO:0000269|PubMed:9632794}.;
Disease
DISEASE: Note=A chromosomal aberration involving CDC5L is found in multicystic renal dysplasia. Translocation t(6;19)(p21;q13.1) with USF2.;

Recessive Scores

pRec
0.160

Intolerance Scores

LoFtool
0.132
RVIS EVS
-0.8
RVIS percentile EVS
12.46

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.975

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
Feedback | API | MCP | Annotate VCF | Sitemap | About | Privacy & Terms
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.