CBY2

chibby family member 2

Basic information

Region (hg38): 13:45702320-45714559

Previous symbols: [ "SPERT" ]

Links

ENSG00000174015 ∙ NCBI:220082 ∙ OMIM:618614 ∙ HGNC:30720 ∙ Uniprot:Q8NA61 ∙ 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 CBY2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBY2 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			37	2		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	37	2	0

Variants in CBY2

This is a list of pathogenic ClinVar variants found in the CBY2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-45702806-A-G		not specified	Uncertain significance (Jan 03, 2022)
13-45702821-G-A		not specified	Uncertain significance (Sep 17, 2021)
13-45702850-C-T		not specified	Uncertain significance (Mar 01, 2023)
13-45713174-T-C			Likely benign (Apr 01, 2023)
13-45713329-C-T		not specified	Uncertain significance (Mar 13, 2023)
13-45713332-A-G		not specified	Uncertain significance (Jun 17, 2022)
13-45713356-G-A		not specified	Uncertain significance (Aug 12, 2021)
13-45713378-C-T		not specified	Uncertain significance (Mar 25, 2024)
13-45713447-G-A		not specified	Uncertain significance (Mar 15, 2024)
13-45713536-G-A		not specified	Uncertain significance (Feb 28, 2024)
13-45713572-C-A		not specified	Uncertain significance (Dec 14, 2023)
13-45713575-G-A		not specified	Uncertain significance (Jun 09, 2022)
13-45713602-A-G		not specified	Uncertain significance (Jan 26, 2022)
13-45713609-T-C		not specified	Uncertain significance (Aug 02, 2022)
13-45713616-G-C		not specified	Uncertain significance (Dec 14, 2023)
13-45713625-G-C		not specified	Uncertain significance (Dec 19, 2023)
13-45713650-C-G		not specified	Uncertain significance (Apr 07, 2023)
13-45713656-G-A		not specified	Uncertain significance (Jun 23, 2021)
13-45713666-C-T		not specified	Uncertain significance (May 03, 2023)
13-45713669-C-G		not specified	Uncertain significance (Dec 13, 2022)
13-45713708-T-C		not specified	Likely benign (Jul 06, 2021)
13-45713737-G-A		not specified	Uncertain significance (Aug 09, 2021)
13-45713744-G-A		not specified	Uncertain significance (Feb 15, 2023)
13-45713831-C-T		not specified	Uncertain significance (Sep 27, 2021)
13-45713885-C-T		not specified	Uncertain significance (Mar 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CBY2	protein_coding	protein_coding	ENST00000310521	3	12249

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000361	0.834	114129	408	11211	125748	0.0473

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.247	248	259	0.957	0.0000174	2878
Missense in Polyphen		98	99.183	0.98807		1124
Synonymous	-0.395	126	120	1.05	0.00000856	892
Loss of Function	1.31	9	14.4	0.626	7.02e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.157	0.152
Ashkenazi Jewish	0.0597	0.0589
East Asian	0.000602	0.000598
Finnish	0.0549	0.0545
European (Non-Finnish)	0.0490	0.0479
Middle Eastern	0.000602	0.000598
South Asian	0.0492	0.0486
Other	0.0504	0.0484

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.782
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.271
• hipred: N
• hipred_score: 0.208
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spert

Gene ontology

• Biological process: negative regulation of Wnt signaling pathway;cilium assembly;ciliary transition zone assembly
• Cellular component: centriole;cytoplasmic vesicle;ciliary basal body
• Molecular function: protein binding