CCPG1

cell cycle progression 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 15:55340031-55408510

Links

ENSG00000260916 ∙ NCBI:9236 ∙ OMIM:611326 ∙ HGNC:24227 ∙ Uniprot:Q9ULG6 ∙ 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 CCPG1 gene.

• Inborn genetic diseases (31 variants)
• not provided (18 variants)
• Developmental and epileptic encephalopathy, 80 (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCPG1 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				1		1
missense			27	2		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			10	7	2	19
Total	0	0	37	10	2

Variants in CCPG1

This is a list of pathogenic ClinVar variants found in the CCPG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-55340602-A-G		Developmental and epileptic encephalopathy, 80	Pathogenic (Jan 07, 2024)
15-55340603-C-T			Likely benign (Sep 21, 2022)
15-55340604-G-A			Uncertain significance (Aug 02, 2022)
15-55340612-T-C			Uncertain significance (Aug 06, 2022)
15-55340618-C-T			Likely benign (Jan 01, 2023)
15-55340621-G-C		Developmental and epileptic encephalopathy, 80	Pathogenic (Oct 20, 2020)
15-55340626-A-G			Likely benign (Nov 12, 2023)
15-55340643-T-G			Uncertain significance (Aug 15, 2022)
15-55340647-C-T			Likely benign (Aug 22, 2022)
15-55340648-G-A			Uncertain significance (Aug 21, 2022)
15-55340650-G-A			Likely benign (Dec 09, 2023)
15-55340661-G-T		Developmental and epileptic encephalopathy, 80 • PIGB-related disorder	Benign (Feb 01, 2024)
15-55340667-C-T		Inborn genetic diseases	Uncertain significance (Aug 05, 2022)
15-55340668-A-C			Likely benign (Dec 13, 2023)
15-55340668-A-G			Likely benign (Nov 13, 2023)
15-55340677-TTCTCATCC-T			Pathogenic (Aug 17, 2023)
15-55340686-A-G			Likely benign (Sep 01, 2022)
15-55340692-C-T			Likely benign (Jul 30, 2023)
15-55340716-A-C			Likely benign (Dec 27, 2023)
15-55340719-T-A			Likely benign (Mar 26, 2023)
15-55340721-T-C		Inborn genetic diseases	Uncertain significance (Oct 13, 2022)
15-55340723-T-C			Likely benign (Aug 24, 2023)
15-55340730-C-T			Uncertain significance (Dec 10, 2021)
15-55340732-C-T			Uncertain significance (Nov 18, 2021)
15-55340732-CACTT-C			Pathogenic (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCPG1	protein_coding	protein_coding	ENST00000442196	8	68479

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000561	0.999	124760	0	34	124794	0.000136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.990	350	406	0.862	0.0000199	5407
Missense in Polyphen		97	149.37	0.64941		2069
Synonymous	-0.722	147	136	1.08	0.00000657	1382
Loss of Function	3.54	12	34.5	0.348	0.00000173	475

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000415	0.000410
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000223
Finnish	0.0000931	0.0000928
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000223	0.000223
South Asian	0.000165	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an assembly platform for Rho protein signaling complexes. Limits guanine nucleotide exchange activity of MCF2L toward RHOA, which results in an inhibition of both its transcriptional activation ability and its transforming activity. Does not inhibit activity of MCF2L toward CDC42, or activity of MCF2 toward either RHOA or CDC42 (By similarity). May be involved in cell cycle regulation. {ECO:0000250, ECO:0000269|PubMed:9383053}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.506
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.87

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.340
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0844

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccpg1

Gene ontology

• Biological process: cell cycle;positive regulation of cell population proliferation;positive regulation of cell cycle;positive regulation of transcription by RNA polymerase II;regulation of Rho guanyl-nucleotide exchange factor activity
• Cellular component: integral component of membrane
• Molecular function: molecular_function;protein binding