C2CD2

C2 calcium dependent domain containing 2, the group of C2 domain containing

Basic information

Region (hg38): 21:41885112-41954018

Previous symbols: [ "C21orf25" ]

Links

ENSG00000157617 ∙ NCBI:25966 ∙ OMIM:617581 ∙ HGNC:1266 ∙ Uniprot:Q9Y426 ∙ 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 C2CD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C2CD2 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				1	4	5
missense			39	4		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	0	0	40	5	4

Variants in C2CD2

This is a list of pathogenic ClinVar variants found in the C2CD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-41889212-G-C		not specified	Uncertain significance (Aug 06, 2024)
21-41889228-G-C		not specified	Uncertain significance (Oct 22, 2021)
21-41889285-G-T		not specified	Uncertain significance (Jan 30, 2024)
21-41889306-G-A		not specified	Uncertain significance (Mar 10, 2025)
21-41889326-C-G		not specified	Uncertain significance (Dec 14, 2024)
21-41889339-T-G		not specified	Uncertain significance (May 30, 2023)
21-41899045-G-A			Benign (Jul 23, 2018)
21-41899103-G-A		not specified	Uncertain significance (Jul 26, 2024)
21-41899130-A-G		not specified	Likely benign (Oct 10, 2023)
21-41899151-G-T		not specified	Uncertain significance (Dec 13, 2022)
21-41899234-G-A			Benign (Jul 23, 2018)
21-41899271-G-A		not specified	Uncertain significance (Jul 27, 2024)
21-41899281-G-A		not specified	Uncertain significance (Jan 17, 2025)
21-41899316-G-A		not specified	Likely benign (Dec 10, 2024)
21-41901660-G-A		not specified	Uncertain significance (Mar 06, 2023)
21-41901672-G-A		not specified	Uncertain significance (Jan 31, 2023)
21-41901707-G-A		not specified	Uncertain significance (Jan 31, 2023)
21-41905760-C-T		not specified	Uncertain significance (Feb 12, 2025)
21-41905765-C-A		not specified	Uncertain significance (Feb 08, 2025)
21-41905813-T-A		not specified	Uncertain significance (May 25, 2022)
21-41905817-T-C		not specified	Likely benign (Aug 23, 2021)
21-41905831-G-A		not specified	Uncertain significance (Sep 26, 2022)
21-41905834-G-C		not specified	Uncertain significance (Aug 19, 2024)
21-41907023-G-A			Benign (Mar 29, 2018)
21-41907028-G-A		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C2CD2	protein_coding	protein_coding	ENST00000380486	14	68779

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000906	0.999	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	336	404	0.831	0.0000246	4451
Missense in Polyphen		90	114.03	0.78926		1385
Synonymous	-0.771	193	180	1.07	0.0000127	1443
Loss of Function	2.98	14	32.2	0.434	0.00000153	378

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000428	0.000427
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000379	0.000378
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0925

Intolerance Scores

• loftool: 0.672
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.32

Haploinsufficiency Scores

• pHI: 0.0840
• hipred: N
• hipred_score: 0.348
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.210

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C2cd2

Gene ontology

• Cellular component: nucleus;cytosol;integral component of membrane