C2CD4B

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

Basic information

Region (hg38): 15:62163535-62165285

Previous symbols: [ "FAM148B" ]

Links

ENSG00000205502 ∙ NCBI:388125 ∙ OMIM:610344 ∙ HGNC:33628 ∙ Uniprot:A6NLJ0 ∙ 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 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	1		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)
15-62163972-G-A		not specified	Uncertain significance (Aug 02, 2021)
15-62164003-C-T		not specified	Uncertain significance (Jul 12, 2023)
15-62164006-C-T		not specified	Uncertain significance (Oct 16, 2024)
15-62164011-G-C		not specified	Uncertain significance (Jun 16, 2023)
15-62164015-G-A		not specified	Uncertain significance (Aug 10, 2021)
15-62164025-G-C		not specified	Uncertain significance (Jan 05, 2022)
15-62164039-C-G		not specified	Uncertain significance (Mar 01, 2025)
15-62164054-G-A		not specified	Uncertain significance (Dec 14, 2021)
15-62164059-C-G		not specified	Uncertain significance (Jun 02, 2024)
15-62164075-T-C		not specified	Uncertain significance (Dec 13, 2023)
15-62164141-G-T		not specified	Uncertain significance (Apr 11, 2023)
15-62164146-G-A		not specified	Uncertain significance (Mar 25, 2024)
15-62164173-C-G		not specified	Uncertain significance (Feb 16, 2023)
15-62164227-C-T		not specified	Uncertain significance (Feb 02, 2022)
15-62164258-C-T		not specified	Uncertain significance (Jun 29, 2022)
15-62164263-C-T		not specified	Uncertain significance (Sep 14, 2023)
15-62164273-C-G		not specified	Uncertain significance (Jul 14, 2024)
15-62164290-G-C		not specified	Uncertain significance (Oct 01, 2024)
15-62164308-G-C		not specified	Uncertain significance (Dec 26, 2023)
15-62164386-C-A		not specified	Uncertain significance (Jan 24, 2024)
15-62164393-G-A		not specified	Uncertain significance (Feb 23, 2023)
15-62164395-G-A		not specified	Uncertain significance (Jan 09, 2025)
15-62164398-A-G		not specified	Uncertain significance (May 08, 2023)
15-62164416-G-C		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C2CD4B	protein_coding	protein_coding	ENST00000380392	1	1749

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000887	0.196	104563	0	3	104566	0.0000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0138	105	105	1.00	0.00000515	2104
Missense in Polyphen		38	38.345	0.991		716
Synonymous	-0.796	56	48.9	1.14	0.00000242	863
Loss of Function	-1.06	5	3.01	1.66	1.29e-7	60

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	0.000111	0.000111
Other	0.00	0.00

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

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

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

Mouse Genome Informatics

• Gene name: C2cd4b

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