CDC40

cell division cycle 40, the group of Spliceosomal Bact complex|Spliceosomal P complex|WD repeat domain containing|NTC associated proteins|Spliceosomal C complex

Basic information

Region (hg38): 6:110180141-110254275

Links

ENSG00000168438 ∙ NCBI:51362 ∙ OMIM:605585 ∙ HGNC:17350 ∙ Uniprot:O60508 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• pontocerebellar hypoplasia, type 15 (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDC40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC40 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						0
missense			14		1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	1

Variants in CDC40

This is a list of pathogenic ClinVar variants found in the CDC40 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-110180448-T-G		not specified	Uncertain significance (Nov 10, 2022)
6-110180551-C-G		not specified	Uncertain significance (Dec 30, 2023)
6-110201609-A-T		not specified	Uncertain significance (Mar 17, 2023)
6-110209092-G-A		not specified	Uncertain significance (Apr 11, 2023)
6-110209120-A-C		not specified	Uncertain significance (May 26, 2024)
6-110209129-A-G		not specified	Uncertain significance (Jan 10, 2022)
6-110210735-C-T		not specified	Uncertain significance (Apr 18, 2023)
6-110210740-A-G		not specified	Uncertain significance (Jun 21, 2023)
6-110213089-G-A		not specified	Uncertain significance (Jan 03, 2024)
6-110215286-C-G			Benign (Jan 01, 2024)
6-110215307-C-T		Pontocerebellar hypoplasia, type 15	Uncertain significance (May 20, 2023)
6-110215310-C-T		not specified	Uncertain significance (Jan 03, 2022)
6-110217749-C-G		not specified	Uncertain significance (Mar 17, 2023)
6-110219368-G-A			Likely benign (Jul 01, 2024)
6-110226222-G-A		not specified	Uncertain significance (Nov 21, 2023)
6-110228855-A-G		not specified	Uncertain significance (Dec 16, 2023)
6-110228919-T-G		Pontocerebellar hypoplasia, type 15 • Congenital pontocerebellar hypoplasia	Pathogenic/Likely pathogenic (Apr 29, 2021)
6-110230037-A-C		not specified	Uncertain significance (Nov 03, 2022)
6-110230051-A-G		not specified	Uncertain significance (Feb 28, 2023)
6-110246110-C-T		not specified	Uncertain significance (Jun 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDC40	protein_coding	protein_coding	ENST00000368932	15	74135

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.979	0.0206	125729	0	8	125737	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.67	172	303	0.568	0.0000141	3819
Missense in Polyphen		40	105.62	0.3787		1326
Synonymous	0.680	94	103	0.915	0.00000472	1043
Loss of Function	4.60	5	33.9	0.147	0.00000159	431

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	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with the spliceosome late in the splicing pathway and may function in the second step of pre-mRNA splicing. {ECO:0000269|PubMed:9830021}.
• Pathway: Spliceosome - Homo sapiens (human);mRNA Processing;Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;mRNA Splicing - Major Pathway;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA Splicing;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.153

Intolerance Scores

• loftool: 0.224
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.281
• hipred: Y
• hipred_score: 0.786
• ghis: 0.587

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdc40

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA export from nucleus;mRNA export from nucleus;RNA splicing;mRNA 3'-end processing
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome
• Molecular function: RNA binding;protein binding