C2CD2L

C2CD2 like

Basic information

Region (hg38): 11:119102198-119118544

Previous symbols: [ "TMEM24" ]

Links

ENSG00000172375 ∙ NCBI:9854 ∙ OMIM:617582 ∙ HGNC:29000 ∙ Uniprot:O14523 ∙ 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 C2CD2L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C2CD2L 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	1
missense			59	2		61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	59	2	1

Variants in C2CD2L

This is a list of pathogenic ClinVar variants found in the C2CD2L region.

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

Position	Type	Phenotype	Significance	ClinVar
11-119102402-A-G			Benign (Jun 16, 2018)
11-119102403-A-C			Benign (Jun 16, 2018)
11-119107769-G-T		not specified	Uncertain significance (Jan 19, 2024)
11-119107853-T-G		not specified	Uncertain significance (Oct 26, 2021)
11-119107857-T-G		not specified	Uncertain significance (Jan 05, 2022)
11-119107869-G-T		not specified	Uncertain significance (Aug 26, 2024)
11-119107875-A-G		not specified	Likely benign (Aug 12, 2021)
11-119107883-C-T		not specified	Uncertain significance (Nov 20, 2023)
11-119107898-G-T		not specified	Uncertain significance (Oct 12, 2024)
11-119107901-G-C		not specified	Uncertain significance (Nov 21, 2024)
11-119107937-T-C		not specified	Uncertain significance (Feb 28, 2023)
11-119107952-C-A			Benign (Dec 31, 2019)
11-119107976-G-T		not specified	Uncertain significance (Oct 16, 2023)
11-119107997-C-T		not specified	Uncertain significance (Nov 08, 2022)
11-119108022-C-G		not specified	Uncertain significance (Jun 04, 2024)
11-119108052-G-A		not specified	Uncertain significance (Jan 26, 2022)
11-119108075-G-A			Likely benign (Aug 01, 2022)
11-119108092-C-G		not specified	Uncertain significance (Oct 14, 2021)
11-119110179-G-A		not specified	Uncertain significance (Dec 13, 2021)
11-119110197-A-G		not specified	Uncertain significance (Oct 07, 2024)
11-119110553-G-A			Benign (Dec 31, 2019)
11-119110594-C-T		not specified	Uncertain significance (Aug 08, 2022)
11-119110622-C-T		not specified	Uncertain significance (Nov 11, 2024)
11-119110627-G-A		not specified	Uncertain significance (Jul 19, 2023)
11-119110640-T-C		not specified	Uncertain significance (Apr 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C2CD2L	protein_coding	protein_coding	ENST00000336702	14	16345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.987	0.0128	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	320	423	0.757	0.0000255	4478
Missense in Polyphen		114	166.74	0.68368		1759
Synonymous	1.24	154	175	0.880	0.0000106	1565
Loss of Function	4.48	4	30.8	0.130	0.00000157	337

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lipid-binding protein that transports phosphatidylinositol, the precursor of phosphatidylinositol 4,5- bisphosphate (PI(4,5)P2), from its site of synthesis in the endoplasmic reticulum to the cell membrane (PubMed:28209843). It thereby maintains the pool of cell membrane phosphoinositides, which are degraded during phospholipase C (PLC) signaling (PubMed:28209843). Plays a key role in the coordination of Ca(2+) and phosphoinositide signaling: localizes to sites of contact between the endoplasmic reticulum and the cell membrane, where it tethers the two bilayers (PubMed:28209843). In response to elevation of cytosolic Ca(2+), it is phosphorylated at its C- terminus and dissociates from the cell membrane, abolishing phosphatidylinositol transport to the cell membrane (PubMed:28209843). Positively regulates insulin secretion in response to glucose: phosphatidylinositol transfer to the cell membrane allows replenishment of PI(4,5)P2 pools and calcium channel opening, priming a new population of insulin granules (PubMed:28209843). {ECO:0000269|PubMed:28209843}.

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.133
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.15

Haploinsufficiency Scores

• pHI: 0.494
• hipred: Y
• hipred_score: 0.662
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.373

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C2cd2l

Gene ontology

• Biological process: phospholipid transport;positive regulation of insulin secretion involved in cellular response to glucose stimulus
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;cortical endoplasmic reticulum;cytoplasmic side of apical plasma membrane
• Molecular function: phospholipid transporter activity;phosphatidylinositol transporter activity;phosphatidylinositol binding;insulin binding