CALCOCO2

calcium binding and coiled-coil domain 2

Basic information

Region (hg38): 17:48831018-48868228

Links

ENSG00000136436 ∙ NCBI:10241 ∙ OMIM:604587 ∙ HGNC:29912 ∙ Uniprot:Q13137 ∙ 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 CALCOCO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALCOCO2 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			17	3		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	0

Variants in CALCOCO2

This is a list of pathogenic ClinVar variants found in the CALCOCO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48841859-G-A		not specified	Uncertain significance (May 08, 2024)
17-48848076-A-G		not specified	Uncertain significance (Jun 21, 2022)
17-48848083-G-A		not specified	Uncertain significance (Feb 17, 2022)
17-48848094-A-G		not specified	Uncertain significance (Apr 10, 2023)
17-48848387-C-T		not specified	Uncertain significance (Dec 23, 2022)
17-48848414-C-T		not specified	Uncertain significance (Nov 14, 2023)
17-48849255-G-A		not specified	Uncertain significance (Mar 31, 2023)
17-48849325-T-A		not specified	Uncertain significance (Jan 17, 2023)
17-48849341-G-T		not specified	Uncertain significance (Mar 19, 2024)
17-48849358-C-T		not specified	Uncertain significance (Mar 23, 2022)
17-48849375-C-A		not specified	Uncertain significance (Jul 14, 2023)
17-48851111-G-A		not specified	Uncertain significance (Dec 19, 2022)
17-48851162-A-C		not specified	Uncertain significance (Feb 16, 2023)
17-48851575-C-G		not specified	Uncertain significance (Apr 08, 2024)
17-48851618-A-G		not specified	Uncertain significance (May 21, 2024)
17-48852603-A-G		not specified	Uncertain significance (Jan 03, 2022)
17-48853011-T-C		not specified	Likely benign (Dec 01, 2022)
17-48856114-A-G		not specified	Likely benign (Dec 09, 2023)
17-48856131-G-A		not specified	Likely benign (Nov 08, 2022)
17-48856147-C-A		not specified	Uncertain significance (Jun 03, 2024)
17-48860348-A-G		not specified	Uncertain significance (Dec 02, 2022)
17-48860432-A-G		not specified	Uncertain significance (May 23, 2023)
17-48862300-G-C		not specified	Uncertain significance (Apr 27, 2023)
17-48862888-C-A		not specified	Uncertain significance (Apr 05, 2023)
17-48862926-A-G		not specified	Uncertain significance (Sep 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALCOCO2	protein_coding	protein_coding	ENST00000448105	13	35535

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000103	0.999	125713	0	32	125745	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.913	197	237	0.833	0.0000113	3161
Missense in Polyphen		48	66.117	0.72599		946
Synonymous	0.638	76	83.4	0.911	0.00000413	751
Loss of Function	3.03	12	29.9	0.401	0.00000133	372

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000732	0.000731
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.0000547	0.0000544
South Asian	0.000327	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Xenophagy-specific receptor required for autophagy- mediated intracellular bacteria degradation. Acts as an effector protein of galectin-sensed membrane damage that restricts the proliferation of infecting pathogens such as Salmonella typhimurium upon entry into the cytosol by targeting LGALS8- associated bacteria for autophagy (PubMed:22246324). Initially orchestrates bacteria targeting to autophagosomes and subsequently ensures pathogen degradation by regulating pathogen-containing autophagosome maturation (PubMed:23022382, PubMed:25771791). Bacteria targeting to autophagosomes relies on its interaction with MAP1LC3A, MAP1LC3B and/or GABARAPL2, whereas regulation of pathogen-containing autophagosome maturation requires the interaction with MAP3LC3C (PubMed:23022382, PubMed:25771791). May play a role in ruffle formation and actin cytoskeleton organization and seems to negatively regulate constitutive secretion (PubMed:17635994). {ECO:0000269|PubMed:17635994, ECO:0000269|PubMed:22246324, ECO:0000269|PubMed:23022382, ECO:0000269|PubMed:23386746, ECO:0000269|PubMed:25771791}.
• Pathway: Mitophagy - animal - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.0584

Intolerance Scores

• loftool: 0.818
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.25

Haploinsufficiency Scores

• pHI: 0.0501
• hipred: N
• hipred_score: 0.493
• ghis: 0.445

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.734

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Calcoco2

Gene ontology

• Biological process: viral process;response to interferon-gamma;xenophagy;positive regulation of autophagosome maturation
• Cellular component: autophagosome membrane;nucleus;cytoplasm;autophagosome;cytosol;cytoskeleton;membrane;cytoplasmic vesicle;intracellular membrane-bounded organelle;perinuclear region of cytoplasm
• Molecular function: protein binding;protein homodimerization activity