CBY3

chibby family member 3

Basic information

Region (hg38): 5:179678560-179681034

Links

ENSG00000204659 ∙ NCBI:646019 ∙ ∙ HGNC:33278 ∙ Uniprot:A6NI87 ∙ 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 CBY3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBY3 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in CBY3

This is a list of pathogenic ClinVar variants found in the CBY3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-179678605-G-A		not specified	Uncertain significance (Apr 06, 2022)
5-179678722-A-G		not specified	Uncertain significance (Jul 29, 2023)
5-179678730-C-T		not specified	Uncertain significance (Aug 22, 2023)
5-179678731-A-T		not specified	Uncertain significance (Jul 25, 2023)
5-179678749-T-A		not specified	Uncertain significance (May 26, 2022)
5-179678771-G-C		not specified	Uncertain significance (May 27, 2022)
5-179678891-T-G		not specified	Uncertain significance (Sep 06, 2022)
5-179678925-G-C		not specified	Uncertain significance (Jan 04, 2022)
5-179678962-C-T		not specified	Uncertain significance (May 30, 2024)
5-179678983-T-C		not specified	Uncertain significance (Mar 12, 2024)
5-179679089-T-C		not specified	Uncertain significance (Oct 13, 2023)
5-179679095-A-C		not specified	Uncertain significance (Aug 02, 2021)
5-179679102-G-T		not specified	Uncertain significance (Dec 13, 2021)
5-179679110-G-A		not specified	Uncertain significance (Oct 27, 2023)
5-179679115-G-A		not specified	Uncertain significance (Jun 24, 2022)
5-179679170-T-A		not specified	Uncertain significance (Jan 19, 2024)
5-179679226-C-T		not specified	Uncertain significance (Apr 18, 2023)
5-179679254-C-T		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CBY3	protein_coding	protein_coding	ENST00000376974	2	2392

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000278	0.571	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.257	136	145	0.940	0.00000766	1526
Missense in Polyphen		30	38.967	0.76989		445
Synonymous	-0.172	69	67.2	1.03	0.00000354	525
Loss of Function	0.540	6	7.61	0.789	3.34e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.41

Haploinsufficiency Scores

• pHI: 0.225

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.149

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cby3

Gene ontology

• Biological process: negative regulation of Wnt signaling pathway;cilium assembly;ciliary transition zone assembly
• Cellular component: centriole;ciliary basal body