CACYBP

calcyclin binding protein

Basic information

Region (hg38): 1:174999163-175012027

Links

ENSG00000116161 ∙ NCBI:27101 ∙ OMIM:606186 ∙ HGNC:30423 ∙ Uniprot:Q9HB71 ∙ 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 CACYBP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CACYBP 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			5			5
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	5	0	2

Variants in CACYBP

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

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

Position	Type	Phenotype	Significance	ClinVar
1-175004761-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-175004777-C-G		not specified	Uncertain significance (Nov 08, 2022)
1-175006836-A-G			Benign (Dec 31, 2019)
1-175007124-T-C		not specified	Uncertain significance (May 31, 2023)
1-175007175-C-G		not specified	Uncertain significance (May 15, 2024)
1-175008688-A-G		not specified	Uncertain significance (Oct 22, 2021)
1-175008715-A-G			Benign (Jul 13, 2018)
1-175010072-A-G		not specified	Uncertain significance (Jan 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CACYBP	protein_coding	protein_coding	ENST00000367679	6	12552

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.920	0.0801	125728	0	9	125737	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	81	115	0.702	0.00000551	1502
Missense in Polyphen		15	30.992	0.484		443
Synonymous	-0.242	43	41.0	1.05	0.00000212	402
Loss of Function	3.01	1	12.5	0.0801	6.08e-7	167

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in calcium-dependent ubiquitination and subsequent proteasomal degradation of target proteins. Probably serves as a molecular bridge in ubiquitin E3 complexes. Participates in the ubiquitin-mediated degradation of beta-catenin (CTNNB1). {ECO:0000269|PubMed:16085652}.
• Pathway: Wnt signaling pathway - Homo sapiens (human);Gastric Cancer Network 2 (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.501
• hipred: Y
• hipred_score: 0.783
• ghis: 0.650

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.858

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cacybp
• Phenotype: immune system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: heart development
• Cellular component: nucleus;nucleoplasm;cytosol;beta-catenin destruction complex;extracellular exosome
• Molecular function: protein binding;tubulin binding;ubiquitin protein ligase binding;protein homodimerization activity;S100 protein binding