CCNDBP1

cyclin D1 binding protein 1

Basic information

Region (hg38): 15:43185118-43197177

Links

ENSG00000166946 ∙ NCBI:23582 ∙ OMIM:607089 ∙ HGNC:1587 ∙ Uniprot:O95273 ∙ 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 CCNDBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCNDBP1 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in CCNDBP1

This is a list of pathogenic ClinVar variants found in the CCNDBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-43185518-C-T		not specified	Uncertain significance (Nov 13, 2023)
15-43185557-A-G		not specified	Uncertain significance (Aug 02, 2021)
15-43185584-G-A		not specified	Uncertain significance (Oct 03, 2024)
15-43185604-C-T		not specified	Uncertain significance (Feb 19, 2025)
15-43185825-G-C		not specified	Uncertain significance (Nov 08, 2022)
15-43185838-C-G		not specified	Uncertain significance (Mar 04, 2024)
15-43186165-G-A		not specified	Uncertain significance (Jan 17, 2024)
15-43186171-G-C		not specified	Uncertain significance (Jan 21, 2025)
15-43186192-C-G		not specified	Uncertain significance (Apr 18, 2023)
15-43186213-C-T		not specified	Uncertain significance (Nov 27, 2023)
15-43189202-A-G		not specified	Uncertain significance (May 27, 2022)
15-43190079-G-A		not specified	Uncertain significance (Dec 27, 2023)
15-43190084-G-A		not specified	Uncertain significance (Feb 25, 2025)
15-43190094-A-G		not specified	Uncertain significance (Feb 23, 2025)
15-43190121-T-C		not specified	Uncertain significance (May 26, 2022)
15-43190351-A-G		not specified	Likely benign (Feb 22, 2025)
15-43190360-T-C		not specified	Uncertain significance (Mar 01, 2024)
15-43190383-C-A		not specified	Uncertain significance (Jan 27, 2025)
15-43190990-T-C		not specified	Uncertain significance (Apr 29, 2024)
15-43191013-G-C		not specified	Uncertain significance (Aug 27, 2024)
15-43191038-A-C		not specified	Uncertain significance (Feb 13, 2025)
15-43191486-G-A		not specified	Uncertain significance (Feb 08, 2023)
15-43191498-A-G		not specified	Uncertain significance (Dec 04, 2024)
15-43191501-A-G		not specified	Likely benign (Apr 04, 2023)
15-43191663-A-C		not specified	Uncertain significance (Dec 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCNDBP1	protein_coding	protein_coding	ENST00000300213	11	10081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000302	0.988	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.332	182	195	0.933	0.00000936	2359
Missense in Polyphen		60	72.215	0.83085		904
Synonymous	1.07	64	75.8	0.844	0.00000398	686
Loss of Function	2.22	9	19.6	0.459	9.18e-7	233

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000849	0.000849
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000217
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.000223	0.000217
South Asian	0.000399	0.000392
Other	0.000839	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May negatively regulate cell cycle progression. May act at least in part via inhibition of the cyclin-D1/CDK4 complex, thereby preventing phosphorylation of RB1 and blocking E2F- dependent transcription. {ECO:0000269|PubMed:10801854}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.691
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.0452
• hipred: Y
• hipred_score: 0.609
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.450

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccndbp1
• Phenotype: liver/biliary system phenotype; neoplasm; cellular phenotype

Gene ontology

• Biological process: cell cycle;regulation of cell cycle
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: protein binding