C2CD4A

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

Basic information

Region (hg38): 15:62066977-62070917

Previous symbols: [ "FAM148A" ]

Links

ENSG00000198535 ∙ NCBI:145741 ∙ OMIM:610343 ∙ HGNC:33627 ∙ Uniprot:Q8NCU7 ∙ 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 C2CD4A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C2CD4A 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			51	2		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	51	2	0

Variants in C2CD4A

This is a list of pathogenic ClinVar variants found in the C2CD4A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-62067624-T-C		not specified	Uncertain significance (Nov 10, 2022)
15-62067627-A-T		not specified	Uncertain significance (Jan 20, 2025)
15-62067648-A-C		not specified	Uncertain significance (Jan 23, 2025)
15-62067666-G-A		not specified	Uncertain significance (Jan 04, 2022)
15-62067675-T-C		not specified	Uncertain significance (Apr 24, 2024)
15-62067683-G-T		not specified	Uncertain significance (Oct 03, 2022)
15-62067687-G-C		not specified	Uncertain significance (Feb 07, 2023)
15-62067714-C-T		not specified	Uncertain significance (Dec 11, 2024)
15-62067744-A-G		not specified	Uncertain significance (Oct 24, 2024)
15-62067795-T-G		not specified	Uncertain significance (Feb 07, 2025)
15-62067836-G-A		not specified	Uncertain significance (Jan 04, 2024)
15-62067852-G-T		not specified	Uncertain significance (Aug 28, 2024)
15-62067897-A-C		Esophageal atresia;Pyloric stenosis	Uncertain significance (May 22, 2019)
15-62067908-G-A		not specified	Uncertain significance (Nov 17, 2022)
15-62067917-G-A		not specified	Uncertain significance (Oct 27, 2022)
15-62067921-A-G		not specified	Uncertain significance (Nov 20, 2024)
15-62067953-A-T		not specified	Uncertain significance (Sep 27, 2022)
15-62067975-T-C		not specified	Uncertain significance (Aug 12, 2021)
15-62067984-G-A		not specified	Likely benign (May 16, 2024)
15-62067987-C-T		not specified	Uncertain significance (Feb 28, 2023)
15-62067990-C-T		not specified	Uncertain significance (Apr 08, 2024)
15-62068032-G-T		not specified	Uncertain significance (May 16, 2024)
15-62068046-C-G		not specified	Uncertain significance (Apr 18, 2023)
15-62068053-C-A		not specified	Uncertain significance (Aug 27, 2024)
15-62068065-C-T		not specified	Uncertain significance (Jul 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C2CD4A	protein_coding	protein_coding	ENST00000355522	1	3941

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0175	0.734	124290	0	12	124302	0.0000483

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.250	144	136	1.06	0.00000637	2184
Missense in Polyphen		52	48.809	1.0654		690
Synonymous	-1.46	78	63.2	1.23	0.00000295	912
Loss of Function	0.756	3	4.78	0.627	2.08e-7	57

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000874	0.0000874
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000624	0.0000472
European (Non-Finnish)	0.0000458	0.0000447
Middle Eastern	0.00	0.00
South Asian	0.0000999	0.0000980
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: 0.103

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C2cd4a

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