CDC7

cell division cycle 7

Basic information

Region (hg38): 1:91500851-91525764

Previous symbols: [ "CDC7L1" ]

Links

ENSG00000097046

∙ NCBI:8317 ∙ OMIM:603311 ∙ HGNC:1745 ∙ Uniprot:O00311 ∙ 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 CDC7 gene.

not_specified (65 variants)
not_provided (2 variants)
Premature_ovarian_insufficiency (1 variants)
Inborn_genetic_diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003503.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			66 clinvar	2 clinvar		68
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDC7	protein_coding	protein_coding	ENST00000428239	11	24914

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000443	0.991	125662	0	86	125748	0.000342

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.686	265	298	0.888	0.0000142	3791
Missense in Polyphen		106	128.65	0.82393		1609
Synonymous	0.648	90	98.2	0.917	0.00000445	1063
Loss of Function	2.35	13	25.9	0.501	0.00000119	349

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000949	0.000917
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000333	0.000326
Finnish	0.000282	0.000277
European (Non-Finnish)	0.000423	0.000413
Middle Eastern	0.000333	0.000326
South Asian	0.000199	0.000196
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Seems to phosphorylate critical substrates that regulate the G1/S phase transition and/or DNA replication. Can phosphorylates MCM2 and MCM3. {ECO:0000269|PubMed:12065429}.;
Pathway: Cell cycle - Homo sapiens (human);Cell Cycle;Retinoblastoma (RB) in Cancer;DNA Replication;Gene expression (Transcription);Transcriptional Regulation by E2F6;Generic Transcription Pathway;RNA Polymerase II Transcription;Activation of ATR in response to replication stress;G2/M Checkpoints;Cell Cycle Checkpoints;Activation of the pre-replicative complex;Mitotic G1-G1/S phases;DNA Replication;IL-7 signaling;JAK STAT pathway and regulation;G1/S Transition;EPO signaling;DNA Replication Pre-Initiation;M/G1 Transition;Cell Cycle;VEGF;Cell Cycle, Mitotic (Consensus)

Recessive Scores

pRec: 0.194

Intolerance Scores

loftool: 0.941
rvis_EVS: -0.2
rvis_percentile_EVS: 38.98

Haploinsufficiency Scores

pHI: 0.898
hipred: Y
hipred_score: 0.758
ghis: 0.610

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.862

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cdc7
Phenotype: embryo phenotype; reproductive system phenotype; 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); normal phenotype; limbs/digits/tail phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;

Gene ontology

Biological process: G1/S transition of mitotic cell cycle;double-strand break repair via break-induced replication;DNA replication;positive regulation of cell population proliferation;positive regulation of nuclear cell cycle DNA replication;positive regulation of G2/M transition of mitotic cell cycle;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;cell cycle phase transition;cell division;negative regulation of G0 to G1 transition
Cellular component: nucleus;nucleoplasm;cytoplasm;intercellular bridge;mitotic spindle
Molecular function: protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding;kinase activity;metal ion binding