CDC5L

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

Basic information

Region (hg38): 6:44387705-44450425

Links

ENSG00000096401 ∙ NCBI:988 ∙ OMIM:602868 ∙ HGNC:1743 ∙ Uniprot:Q99459 ∙ 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 CDC5L gene.

• not provided (26 variants)
• Inborn genetic diseases (19 variants)
• CDC5L-related condition (3 variants)
• Congenital anomaly of kidney and urinary tract (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC5L 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					4	4
missense			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		2	3
non coding					18	18
Total	0	0	22	2	22

Variants in CDC5L

This is a list of pathogenic ClinVar variants found in the CDC5L region.

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

Position	Type	Phenotype	Significance	ClinVar
6-44387817-C-T		CDC5L-related disorder	Likely benign (Apr 12, 2019)
6-44387822-A-G		CDC5L-related disorder	Likely benign (Aug 18, 2023)
6-44387945-G-A			Benign (Nov 10, 2018)
6-44387962-T-C			Benign (Nov 10, 2018)
6-44390147-T-G			Benign (Jun 18, 2021)
6-44390288-G-A		CDC5L-related disorder	Likely benign (Jun 04, 2019)
6-44390369-A-G		CDC5L-related disorder	Uncertain significance (Jul 10, 2023)
6-44390707-T-G			Benign (Nov 10, 2018)
6-44392418-T-A			Benign (Jun 18, 2021)
6-44392728-C-G		not specified	Uncertain significance (Apr 28, 2022)
6-44392754-A-G		CDC5L-related disorder	Likely benign (Mar 05, 2021)
6-44392796-G-A			Benign (Jun 09, 2021)
6-44392943-A-G			Benign (Nov 10, 2018)
6-44393558-A-G		not specified	Uncertain significance (Jan 20, 2023)
6-44393572-G-A			Benign (Aug 01, 2023)
6-44396346-C-T		not specified	Uncertain significance (Jul 26, 2021)
6-44396427-T-C		CDC5L-related disorder	Likely benign (Nov 26, 2019)
6-44403855-A-T		not specified	Uncertain significance (Mar 27, 2023)
6-44403874-G-A		not specified	Uncertain significance (Aug 09, 2021)
6-44403874-G-C		not specified	Uncertain significance (Nov 03, 2022)
6-44403919-A-C		not specified	Uncertain significance (Feb 07, 2023)
6-44403967-A-G			Uncertain significance (Feb 26, 2018)
6-44403977-C-T			Benign (Nov 10, 2018)
6-44406319-A-G			Benign (Aug 01, 2023)
6-44406339-G-A		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDC5L	protein_coding	protein_coding	ENST00000371477	16	62902

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.68e-7	125697	0	6	125703	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.78	268	430	0.623	0.0000227	5267
Missense in Polyphen		32	126.88	0.25221		1543
Synonymous	-0.729	158	147	1.08	0.00000752	1487
Loss of Function	6.21	2	48.8	0.0410	0.00000302	548

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.00000887	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Recessive Scores

• pRec: 0.160

Intolerance Scores

• loftool: 0.132
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.46

Haploinsufficiency Scores

• pHI: 0.822
• hipred: Y
• hipred_score: 0.827
• ghis: 0.662

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.975

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdc5l

Gene ontology

• 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;cellular response to interleukin-2;signal transduction involved in DNA damage checkpoint;cellular response to wortmannin;cellular response to nerve growth factor stimulus;cellular response to prolactin
• Cellular component: Prp19 complex;nucleus;nucleoplasm;DNA replication factor A complex;cytoplasm;membrane;nuclear speck;perinuclear region of cytoplasm;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome
• 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;RNA binding;protein binding;protein phosphatase 1 binding;protein kinase binding;leucine zipper domain binding;WD40-repeat domain binding