CABYR

calcium binding tyrosine phosphorylation regulated

Basic information

Region (hg38): 18:24138987-24161600

Links

ENSG00000154040NCBI:26256OMIM:612135HGNC:15569Uniprot:O75952AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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
28
clinvar
28
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 29 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
18-24143134-G-T not specified Uncertain significance (May 02, 2024)3262660
18-24155724-A-T not specified Uncertain significance (May 13, 2022)2285625
18-24155727-C-T not specified Uncertain significance (May 11, 2022)2289045
18-24155778-T-C not specified Uncertain significance (May 15, 2024)3262667
18-24155781-A-G not specified Uncertain significance (Sep 01, 2021)2283536
18-24155844-T-A not specified Uncertain significance (Feb 17, 2024)3136265
18-24155890-G-A not specified Uncertain significance (Feb 28, 2023)2491372
18-24155916-G-A not specified Uncertain significance (Apr 14, 2022)2393488
18-24155945-G-C not specified Uncertain significance (Jun 04, 2024)3262662
18-24155973-C-T not specified Uncertain significance (Nov 18, 2022)2391318
18-24156003-G-A not specified Uncertain significance (May 18, 2023)2548845
18-24156111-G-A not specified Uncertain significance (May 26, 2023)2551975
18-24156147-G-A not specified Uncertain significance (Sep 01, 2021)2383247
18-24156169-C-T not specified Uncertain significance (Feb 21, 2024)3136266
18-24156197-A-C not specified Uncertain significance (Oct 29, 2021)2258127
18-24156228-G-A not specified Uncertain significance (Oct 13, 2023)3136267
18-24156241-C-T not specified Uncertain significance (Feb 27, 2024)3136268
18-24156247-C-T not specified Uncertain significance (Dec 11, 2023)3136269
18-24156274-C-T not specified Uncertain significance (Nov 05, 2021)2371172
18-24156297-G-A not specified Uncertain significance (Apr 26, 2024)3262659
18-24156336-G-T not specified Uncertain significance (Sep 15, 2021)2249432
18-24156344-G-T not specified Uncertain significance (Sep 27, 2021)2252078
18-24156348-G-C not specified Uncertain significance (Feb 21, 2024)3136270
18-24156379-T-C not specified Uncertain significance (Jan 10, 2023)2475375
18-24156400-T-G not specified Uncertain significance (Apr 09, 2024)3262665

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CABYRprotein_codingprotein_codingENST00000399496 422626
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000002260.7331242755614171257480.00587
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4101842000.9190.000009882441
Missense in Polyphen6878.6830.864231033
Synonymous0.4456973.90.9340.00000413783
Loss of Function1.181116.10.6827.86e-7204

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.08320.0814
Ashkenazi Jewish0.00009920.0000992
East Asian0.0003260.000326
Finnish0.00004620.0000462
European (Non-Finnish)0.0006290.000624
Middle Eastern0.0003260.000326
South Asian0.0004370.000425
Other0.003340.00326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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