C2CD4B

C2 calcium dependent domain containing 4B, the group of C2 domain containing

Basic information

Region (hg38): 15:62163535-62165285

Previous symbols: [ "FAM148B" ]

Links

ENSG00000205502NCBI:388125OMIM:610344HGNC:33628Uniprot:A6NLJ0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C2CD4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C2CD4B 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
56
clinvar
1
clinvar
57
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 56 1 0

Variants in C2CD4B

This is a list of pathogenic ClinVar variants found in the C2CD4B region.

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

Position Type Phenotype Significance ClinVar
15-62163967-C-G not specified Uncertain significance (Feb 22, 2025)3826306
15-62163972-G-A not specified Uncertain significance (Aug 02, 2021)2240917
15-62164003-C-T not specified Uncertain significance (Jul 12, 2023)2611093
15-62164006-C-T not specified Uncertain significance (Oct 16, 2024)3483545
15-62164011-G-C not specified Uncertain significance (Jun 16, 2023)2590514
15-62164015-G-A not specified Uncertain significance (Aug 10, 2021)2242653
15-62164025-G-C not specified Uncertain significance (Jan 05, 2022)2270508
15-62164039-C-G not specified Uncertain significance (Mar 01, 2025)3826308
15-62164054-G-A not specified Uncertain significance (Dec 14, 2021)2266871
15-62164059-C-G not specified Uncertain significance (Jun 02, 2024)3262473
15-62164075-T-C not specified Uncertain significance (Dec 13, 2023)2355194
15-62164141-G-T not specified Uncertain significance (Apr 11, 2023)2513502
15-62164146-G-A not specified Uncertain significance (Mar 25, 2024)3262468
15-62164173-C-G not specified Uncertain significance (Feb 16, 2023)2467491
15-62164227-C-T not specified Uncertain significance (Feb 02, 2022)2219284
15-62164258-C-T not specified Uncertain significance (Jun 29, 2022)2298698
15-62164263-C-T not specified Uncertain significance (Sep 14, 2023)2624023
15-62164273-C-G not specified Uncertain significance (Jul 14, 2024)3483543
15-62164290-G-C not specified Uncertain significance (Oct 01, 2024)3483544
15-62164308-G-C not specified Uncertain significance (Dec 26, 2023)3135894
15-62164386-C-A not specified Uncertain significance (Jan 24, 2024)3135892
15-62164393-G-A not specified Uncertain significance (Feb 23, 2023)2467986
15-62164395-G-A not specified Uncertain significance (Jan 09, 2025)3826310
15-62164398-A-G not specified Uncertain significance (May 08, 2023)2518729
15-62164416-G-C not specified Uncertain significance (Dec 03, 2021)2263781

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
C2CD4Bprotein_codingprotein_codingENST00000380392 11749
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00008870.196104563031045660.0000143
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.01381051051.000.000005152104
Missense in Polyphen3838.3450.991716
Synonymous-0.7965648.91.140.00000242863
Loss of Function-1.0653.011.661.29e-760

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.0001110.000111
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May be involved in inflammatory process. May regulate cell architecture and adhesion. {ECO:0000269|PubMed:15527968}.;

Recessive Scores

pRec
0.101

Haploinsufficiency Scores

pHI
0.116
hipred
N
hipred_score
0.227
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.114

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
C2cd4b
Phenotype

Zebrafish Information Network

Gene name
c2cd4a
Affected structure
pancreatic B cell
Phenotype tag
abnormal
Phenotype quality
decreased area

Gene ontology

Biological process
regulation of vascular permeability involved in acute inflammatory response;positive regulation of acute inflammatory response;regulation of cell adhesion
Cellular component
nucleus
Molecular function