C2CD5

C2 calcium dependent domain containing 5, the group of C2 domain containing

Basic information

Region (hg38): 12:22448583-22544546

Previous symbols: [ "KIAA0528" ]

Links

ENSG00000111731 ∙ NCBI:9847 ∙ OMIM:618044 ∙ HGNC:29062 ∙ Uniprot:Q86YS7 ∙ 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 C2CD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C2CD5 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			45			45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	0	0

Variants in C2CD5

This is a list of pathogenic ClinVar variants found in the C2CD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-22449771-C-T		not specified	Uncertain significance (May 05, 2023)
12-22453933-T-C		not specified	Uncertain significance (Sep 03, 2024)
12-22454009-T-C		not specified	Uncertain significance (Aug 16, 2021)
12-22457063-T-C		not specified	Uncertain significance (Feb 22, 2024)
12-22457069-T-C		not specified	Uncertain significance (May 02, 2023)
12-22457075-C-T		not specified	Uncertain significance (May 27, 2022)
12-22457110-C-T		not specified	Uncertain significance (Nov 09, 2022)
12-22457117-G-A		not specified	Uncertain significance (Apr 07, 2022)
12-22457134-A-G		not specified	Uncertain significance (Apr 11, 2023)
12-22457135-C-G		not specified	Uncertain significance (Sep 01, 2021)
12-22457155-G-T		not specified	Uncertain significance (Nov 13, 2024)
12-22457161-G-A		not specified	Uncertain significance (Nov 10, 2024)
12-22469730-G-C		not specified	Uncertain significance (Feb 27, 2023)
12-22469744-T-C		not specified	Uncertain significance (Oct 29, 2024)
12-22469792-G-A		not specified	Uncertain significance (Jan 05, 2022)
12-22470832-A-C		not specified	Uncertain significance (Feb 21, 2024)
12-22470862-T-G		not specified	Uncertain significance (Jul 10, 2024)
12-22470874-T-G		not specified	Uncertain significance (Mar 29, 2023)
12-22471430-G-T		not specified	Uncertain significance (Nov 14, 2024)
12-22472004-T-C		not specified	Uncertain significance (Dec 20, 2023)
12-22472010-G-C		not specified	Uncertain significance (Feb 10, 2022)
12-22472315-C-T		not specified	Uncertain significance (Jul 26, 2022)
12-22474789-C-T		not specified	Uncertain significance (Nov 13, 2024)
12-22474812-C-A		not specified	Uncertain significance (Nov 25, 2024)
12-22474820-T-G		not specified	Uncertain significance (Mar 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C2CD5	protein_coding	protein_coding	ENST00000333957	24	95964

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.73e-12	1.00	125673	0	75	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.68	353	526	0.671	0.0000262	6525
Missense in Polyphen		48	104.29	0.46026		1233
Synonymous	-1.48	211	185	1.14	0.00000942	1928
Loss of Function	3.29	27	52.8	0.511	0.00000275	660

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00110
Ashkenazi Jewish	0.00	0.00
East Asian	0.000448	0.000435
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000276	0.000264
Middle Eastern	0.000448	0.000435
South Asian	0.000263	0.000261
Other	0.000493	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for insulin-stimulated glucose transport and glucose transporter SLC2A4/GLUT4 translocation from intracellular glucose storage vesicle (GSV) to the plasma membrane (PM) in adipocytes. Binds phospholipid membranes in a calcium-dependent manner and is necessary for the optimal membrane fusion between SLC2A4/GLUT4 GSV and the PM. {ECO:0000269|PubMed:21907143}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Translocation of GLUT4 to the plasma membrane (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.02

Haploinsufficiency Scores

• pHI: 0.617
• hipred: Y
• hipred_score: 0.575
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C2cd5

Gene ontology

• Biological process: vesicle fusion;positive regulation of glucose transmembrane transport;positive regulation of vesicle fusion;cellular response to insulin stimulus;insulin receptor signaling pathway via phosphatidylinositol 3-kinase;positive regulation of glucose import;intracellular protein transmembrane transport;protein localization to plasma membrane;positive regulation of protein targeting to membrane
• Cellular component: microtubule organizing center;cytosol;plasma membrane;cell cortex;cytoplasmic vesicle membrane;ruffle membrane
• Molecular function: calcium ion binding;calcium-dependent phospholipid binding