C2CD4B

protein-coding

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

Gene summary

Involved in positive regulation of acute inflammatory response; regulation of cell adhesion; and regulation of vascular permeability involved in acute inflammatory response. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FAM148B

MANE transcript

NM_001007595.3

Inheritance

—

ClinVar variants

U:99B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.66

Max pathogenic AF

—

Genomic locus

chr15:62,163,535-62,165,285

External References & Databases

Ensembl (ENSG00000205502)

Transcript & Mutation Effects

hg38 • Region Span ~1.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to C2CD4B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 105

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001007595.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			99 clinvar	7 clinvar		106
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	99	7	0	106

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001007595.3	RefSeq	NP_001007596.2	1	MANE Select
ENST00000380392.4	Ensembl	ENSP00000369755.3	1	MANE Select
ENST00000948855.1	Ensembl	ENSP00000618914.1	1	Standard
ENST00000948855.2	Ensembl	ENSP00000618914.1	1	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
c2cd4a	Danio rerio	Structure: pancreatic B cell Quality: decreased area abnormal

Gene / Model

Organism

Observed Phenotype

c2cd4a

Danio rerio

Structure: pancreatic B cell

Quality: decreased area

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of vascular permeability involved in acute inflammatory response
positive regulation of acute inflammatory response
regulation of cell adhesion

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380392
Coding exons: 1
Length: 1749
Individuals with no LoFs: 104563
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 104566
p: 0.0000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0138	105	105	1.00	0.00000515	2104
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.00011	0.00011	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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