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.

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.

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			31	2		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	31	2	1

Variants in CDC7

This is a list of pathogenic ClinVar variants found in the CDC7 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-91500888-A-G			Benign (Oct 16, 2019)
1-91501738-C-G		not specified	Uncertain significance (Jan 18, 2022)
1-91501814-A-G		not specified	Uncertain significance (Sep 28, 2022)
1-91501828-G-A		not specified	Uncertain significance (May 01, 2024)
1-91501829-C-A		not specified	Uncertain significance (May 01, 2024)
1-91507937-G-A			Uncertain significance (Jun 11, 2021)
1-91508273-T-A		not specified	Uncertain significance (Jan 04, 2022)
1-91508274-C-G		not specified	Uncertain significance (Jul 27, 2021)
1-91508309-C-T		not specified	Uncertain significance (May 30, 2024)
1-91511794-C-T		not specified	Uncertain significance (Jun 29, 2023)
1-91511810-A-C		not specified	Uncertain significance (Sep 29, 2022)
1-91511851-G-A		not specified	Uncertain significance (Aug 31, 2022)
1-91511868-A-G		not specified	Uncertain significance (Nov 06, 2023)
1-91511911-G-A		not specified	Uncertain significance (Feb 23, 2023)
1-91511913-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-91513086-C-G		not specified	Uncertain significance (Jun 22, 2024)
1-91513096-A-G		not specified	Uncertain significance (Jan 27, 2022)
1-91513109-A-G			Likely benign (Nov 01, 2023)
1-91513120-A-C		not specified	Uncertain significance (Aug 13, 2021)
1-91513135-A-C		not specified	Uncertain significance (Mar 02, 2023)
1-91513165-AATCCCAC-A		Premature ovarian insufficiency	Uncertain significance (Jan 10, 2018)
1-91513173-A-G		not specified	Likely benign (Jul 13, 2022)
1-91513197-C-G		not specified	Uncertain significance (Jul 11, 2023)
1-91513232-G-T		not specified	Uncertain significance (Dec 03, 2021)
1-91513246-C-G		Inborn genetic diseases	Uncertain significance (Jun 16, 2016)

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