CBY1

chibby family member 1, beta catenin antagonist

Basic information

Region (hg38): 22:38656636-38673854

Previous symbols: [ "C22orf2", "PGEA1" ]

Links

ENSG00000100211

∙ NCBI:25776 ∙ OMIM:607757 ∙ HGNC:1307 ∙ Uniprot:Q9Y3M2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Joubert syndrome (Supportive), mode of inheritance: AR
ciliopathy (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CBY1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBY1 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			1 clinvar			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1 clinvar			1
Total	0	0	2	0	0

Variants in CBY1

This is a list of pathogenic ClinVar variants found in the CBY1 region.

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

Position	Phenotype	Significance	ClinVar
22-38668022-G-A	Inborn genetic diseases	Uncertain significance (Jul 06, 2021)	2234838
22-38668111-A-ATC	Familial aplasia of the vermis	Pathogenic (Jan 01, 2018)	694265
22-38670951-G-A	Inborn genetic diseases	Uncertain significance (Sep 01, 2021)	2221255
22-38671072-A-G	Inborn genetic diseases	Uncertain significance (Apr 22, 2024)	3263692
22-38671073-CAG-C	Familial aplasia of the vermis	Pathogenic (Jan 01, 2020)	694056
22-38673201-C-G	Malignant tumor of prostate	Uncertain significance (-)	161693

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CBY1	protein_coding	protein_coding	ENST00000396811	4	17219

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00126	0.658	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.438	69	80.0	0.862	0.00000532	810
Missense in Polyphen		14	21.834	0.64121		273
Synonymous	0.348	29	31.5	0.921	0.00000186	249
Loss of Function	0.659	5	6.86	0.729	3.57e-7	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.000272	0.000272
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Inhibits the Wnt/Wingless pathway by binding to CTNNB1/beta-catenin and inhibiting beta-catenin-mediated transcriptional activation through competition with TCF/LEF transcription factors. Has also been shown to play a role in regulating the intracellular trafficking of polycystin-2/PKD2 and possibly of other intracellular proteins. Promotes adipocyte and cardiomyocyte differentiation. {ECO:0000269|PubMed:12712206, ECO:0000269|PubMed:15194699}.;
Pathway: WNT-Ncore;Signaling by WNT;Signal Transduction;Deactivation of the beta-catenin transactivating complex;Wnt Canonical;Regulation of nuclear beta catenin signaling and target gene transcription;TCF dependent signaling in response to WNT;Wnt Mammals (Consensus)

Recessive Scores

pRec: 0.132

Intolerance Scores

loftool: 0.514
rvis_EVS: -0.21
rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

pHI: 0.0905
hipred: Y
hipred_score: 0.523
ghis: 0.621

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.980

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cby1
Phenotype: cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); respiratory system phenotype; immune system phenotype; hearing/vestibular/ear phenotype; hematopoietic system 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);

Gene ontology

Biological process: protein localization;negative regulation of Wnt signaling pathway;fat cell differentiation;negative regulation of transcription, DNA-templated;protein homotetramerization;cardiac muscle cell differentiation;cilium assembly;ciliary transition zone assembly
Cellular component: nucleus;nucleoplasm;trans-Golgi network;centriole;cytosol;nuclear speck;ciliary basal body
Molecular function: protein binding;beta-catenin binding;identical protein binding;protein homodimerization activity