CACUL1

CDK2 associated cullin domain 1

Basic information

Region (hg38): 10:118674167-118755249

Previous symbols: [ "C10orf46" ]

Links

ENSG00000151893 ∙ NCBI:143384 ∙ OMIM:618764 ∙ HGNC:23727 ∙ Uniprot:Q86Y37 ∙ 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 CACUL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CACUL1 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in CACUL1

This is a list of pathogenic ClinVar variants found in the CACUL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-118686162-G-A		not specified	Uncertain significance (Dec 11, 2024)
10-118691283-A-G		not specified	Uncertain significance (Sep 10, 2024)
10-118691378-TAG-T		Flexion contracture	Likely pathogenic (-)
10-118701338-T-C		not specified	Uncertain significance (Feb 24, 2025)
10-118707551-T-C		not specified	Uncertain significance (Mar 30, 2024)
10-118729306-T-C		not specified	Uncertain significance (Oct 12, 2021)
10-118730324-G-A		not specified	Uncertain significance (Feb 24, 2025)
10-118730365-G-C		not specified	Uncertain significance (Jan 17, 2025)
10-118754433-G-C		not specified	Uncertain significance (Jan 04, 2022)
10-118754447-C-T		not specified	Uncertain significance (Jan 26, 2023)
10-118754459-T-C		not specified	Uncertain significance (Oct 25, 2023)
10-118754480-C-G		not specified	Uncertain significance (Dec 14, 2021)
10-118754495-T-A		not specified	Uncertain significance (Jan 22, 2025)
10-118754498-T-C		not specified	Uncertain significance (Apr 06, 2023)
10-118754512-G-T		not specified	Uncertain significance (Mar 25, 2024)
10-118754530-G-A		not specified	Uncertain significance (Feb 08, 2025)
10-118754558-C-T		not specified	Uncertain significance (Dec 27, 2023)
10-118754576-C-T		not specified	Uncertain significance (Jun 03, 2022)
10-118754585-C-G		not specified	Uncertain significance (Jan 06, 2023)
10-118754641-G-C		not specified	Uncertain significance (Sep 08, 2024)
10-118754668-A-C		not specified	Uncertain significance (Oct 01, 2024)
10-118754680-G-C		not specified	Uncertain significance (Jan 25, 2024)
10-118754708-C-T		not specified	Uncertain significance (Dec 21, 2023)
10-118754738-C-T		not specified	Uncertain significance (Apr 30, 2024)
10-118754740-T-A		not specified	Uncertain significance (Aug 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CACUL1	protein_coding	protein_coding	ENST00000369151	9	81083

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.963	0.0368	124788	0	5	124793	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.651	175	201	0.871	0.00000941	2423
Missense in Polyphen		24	44.42	0.5403		588
Synonymous	-0.610	83	76.2	1.09	0.00000392	685
Loss of Function	3.63	2	19.1	0.105	9.04e-7	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000723	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000485	0.0000464
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.0000372	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell cycle associated protein capable of promoting cell proliferation through the activation of CDK2 at the G1/S phase transition. {ECO:0000269|PubMed:19829063}.

Intolerance Scores

• rvis_EVS: -0.63
• rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

• pHI: 0.363
• hipred: Y
• hipred_score: 0.699
• ghis: 0.655

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cacul1

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;ubiquitin-dependent protein catabolic process;positive regulation of cell population proliferation;positive regulation of protein kinase activity
• Molecular function: protein binding;protein kinase binding;ubiquitin protein ligase binding