CDC123

protein-coding

cell division cycle 123

Gene summary

Enables ATP binding activity and magnesium ion binding activity. Involved in eukaryotic translation initiation factor 2 complex assembly. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C10orf7

MANE transcript

NM_006023.3

Inheritance

—

ClinVar variants

U:49B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr10:12,195,965-12,250,589

External References & Databases

Ensembl (ENSG00000151465)

Transcript & Mutation Effects

hg38 • Region Span ~54.6 kb

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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 CDC123 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 37

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006023.3. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			39 clinvar	1 clinvar		40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	49	2	0	51

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 46 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006023.3	RefSeq	NP_006014.2	13	MANE Select
ENST00000281141.9	Ensembl	ENSP00000281141.4	13	MANE Select
ENST00000378900.6	Ensembl	ENSP00000368178.2	12	Standard
ENST00000378900.7	Ensembl	ENSP00000368178.2	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000281141
Coding exons: 13
Length: 54625
Individuals with no LoFs: 125709
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 125747
p: 0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.10	143	185	0.773	0.00000968	2256
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00022	0.00020	rare
South Asian	0.000066	0.000065	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.424

Gene Damage Prediction

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