CABYR

calcium binding tyrosine phosphorylation regulated

Basic information

Region (hg38): 18:24138986-24161600

Links

ENSG00000154040 ∙ NCBI:26256 ∙ OMIM:612135 ∙ HGNC:15569 ∙ Uniprot:O75952 ∙ 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 CABYR gene.

• Inborn genetic diseases (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CABYR 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			21			21
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	22	0	0

Variants in CABYR

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

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

Position	Type	Phenotype	Significance	ClinVar
18-24155724-A-T		not specified	Uncertain significance (May 13, 2022)
18-24155727-C-T		not specified	Uncertain significance (May 11, 2022)
18-24155781-A-G		not specified	Uncertain significance (Sep 01, 2021)
18-24155844-T-A		not specified	Uncertain significance (Feb 17, 2024)
18-24155890-G-A		not specified	Uncertain significance (Feb 28, 2023)
18-24155916-G-A		not specified	Uncertain significance (Apr 14, 2022)
18-24155973-C-T		not specified	Uncertain significance (Nov 18, 2022)
18-24156003-G-A		not specified	Uncertain significance (May 18, 2023)
18-24156111-G-A		not specified	Uncertain significance (May 26, 2023)
18-24156147-G-A		not specified	Uncertain significance (Sep 01, 2021)
18-24156169-C-T		not specified	Uncertain significance (Feb 21, 2024)
18-24156197-A-C		not specified	Uncertain significance (Oct 29, 2021)
18-24156228-G-A		not specified	Uncertain significance (Oct 13, 2023)
18-24156241-C-T		not specified	Uncertain significance (Feb 27, 2024)
18-24156247-C-T		not specified	Uncertain significance (Dec 11, 2023)
18-24156274-C-T		not specified	Uncertain significance (Nov 05, 2021)
18-24156336-G-T		not specified	Uncertain significance (Sep 15, 2021)
18-24156344-G-T		not specified	Uncertain significance (Sep 27, 2021)
18-24156348-G-C		not specified	Uncertain significance (Feb 21, 2024)
18-24156379-T-C		not specified	Uncertain significance (Jan 10, 2023)
18-24156466-A-G		not specified	Uncertain significance (May 27, 2022)
18-24156487-A-C		not specified	Uncertain significance (Feb 16, 2023)
18-24156487-A-G		not specified	Uncertain significance (Jun 03, 2022)
18-24156497-G-C		not specified	Uncertain significance (Oct 12, 2021)
18-24156612-A-T		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CABYR	protein_coding	protein_coding	ENST00000399496	4	22626

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000226	0.733	124275	56	1417	125748	0.00587

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.410	184	200	0.919	0.00000988	2441
Missense in Polyphen		68	78.683	0.86423		1033
Synonymous	0.445	69	73.9	0.934	0.00000413	783
Loss of Function	1.18	11	16.1	0.682	7.86e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0832	0.0814
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000326	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000629	0.000624
Middle Eastern	0.000326	0.000326
South Asian	0.000437	0.000425
Other	0.00334	0.00326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a regulator of both motility- and head- associated functions such as capacitation and the acrosome reaction. Isoform 1 binds calcium in vitro. Isoform 2 and isoform 6 probably bind calcium. Isoform 3 and isoform 5 do not bind calcium in vitro. Isoform 4 probably does not bind calcium.

Recessive Scores

• pRec: 0.0546

Intolerance Scores

• loftool: 0.731
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.0321
• hipred: N
• hipred_score: 0.123
• ghis: 0.381

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0322

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cabyr
• Phenotype: reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: epithelial cilium movement;sperm capacitation
• Cellular component: nucleus;cytoplasm;cytosol;cytoskeleton;motile cilium;sperm fibrous sheath;sperm principal piece;sperm end piece
• Molecular function: calcium ion binding;SH3 domain binding;protein heterodimerization activity