CDC123

cell division cycle 123

Basic information

Region (hg38): 10:12195965-12250589

Previous symbols: [ "C10orf7" ]

Links

ENSG00000151465 ∙ NCBI:8872 ∙ OMIM:617708 ∙ HGNC:16827 ∙ Uniprot:O75794 ∙ 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 CDC123 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC123 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			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	14	0	0

Variants in CDC123

This is a list of pathogenic ClinVar variants found in the CDC123 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-12196264-C-T		not specified	Uncertain significance (Aug 02, 2023)
10-12196304-G-T		not specified	Uncertain significance (Apr 11, 2023)
10-12198721-C-T		not specified	Uncertain significance (Nov 18, 2022)
10-12209991-G-T		not specified	Uncertain significance (Apr 07, 2023)
10-12210292-G-T		not specified	Uncertain significance (Nov 21, 2024)
10-12210321-C-T		not specified	Uncertain significance (Dec 27, 2023)
10-12215752-C-T		not specified	Uncertain significance (Oct 01, 2024)
10-12215786-A-G		not specified	Uncertain significance (May 14, 2024)
10-12217365-C-T		not specified	Uncertain significance (Mar 18, 2024)
10-12217388-T-C		not specified	Uncertain significance (Aug 01, 2024)
10-12217451-C-G		not specified	Uncertain significance (Feb 03, 2022)
10-12217452-G-A		not specified	Uncertain significance (Oct 25, 2023)
10-12230952-A-G		not specified	Uncertain significance (Aug 14, 2024)
10-12230983-G-A		not specified	Uncertain significance (Mar 07, 2023)
10-12230999-A-C			Benign (Jun 20, 2018)
10-12237207-G-T		not specified	Uncertain significance (Sep 01, 2021)
10-12238469-T-C		not specified	Uncertain significance (Jan 24, 2024)
10-12246152-A-G		not specified	Uncertain significance (Apr 22, 2022)
10-12246226-A-G		not specified	Uncertain significance (Mar 24, 2023)
10-12246266-G-A		not specified	Uncertain significance (Mar 01, 2024)
10-12249577-A-G			Benign (Jul 20, 2018)
10-12249588-C-T		not specified	Uncertain significance (Jun 18, 2021)
10-12249677-A-G		not specified	Uncertain significance (Dec 02, 2024)
10-12249689-G-A		not specified	Uncertain significance (Nov 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDC123	protein_coding	protein_coding	ENST00000281141	13	54625

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000111	0.989	125709	0	38	125747	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	143	185	0.773	0.00000968	2256
Missense in Polyphen		39	58.252	0.6695		745
Synonymous	-0.338	69	65.5	1.05	0.00000388	565
Loss of Function	2.27	12	24.0	0.500	0.00000127	258

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000271	0.000271
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.000188	0.000185
European (Non-Finnish)	0.000221	0.000202
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000660	0.0000653
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for S phase entry of the cell cycle. {ECO:0000250}.

Intolerance Scores

• loftool: 0.336
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.173
• hipred: Y
• hipred_score: 0.554
• ghis: 0.657

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.424

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdc123
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); pigmentation phenotype; 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype

Gene ontology

• Biological process: cell cycle arrest;positive regulation of cell population proliferation;positive regulation of translational initiation;cell division;eukaryotic translation initiation factor 2 complex assembly
• Cellular component: cytoplasm