CALCOCO1

calcium binding and coiled-coil domain 1

Basic information

Region (hg38): 12:53708516-53727745

Links

ENSG00000012822 ∙ NCBI:57658 ∙ ∙ HGNC:29306 ∙ Uniprot:Q9P1Z2 ∙ 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 CALCOCO1 gene.

• Inborn genetic diseases (34 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALCOCO1 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			32	2		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	3	0

Variants in CALCOCO1

This is a list of pathogenic ClinVar variants found in the CALCOCO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-53711949-C-G		not specified	Uncertain significance (Sep 01, 2021)
12-53712071-G-T		not specified	Uncertain significance (Jun 29, 2023)
12-53712084-C-T		not specified	Uncertain significance (Nov 17, 2023)
12-53712095-T-C		not specified	Uncertain significance (Mar 13, 2023)
12-53713125-C-G		not specified	Uncertain significance (Jul 12, 2022)
12-53713184-A-C		not specified	Uncertain significance (Oct 12, 2022)
12-53713789-C-T		not specified	Uncertain significance (Sep 13, 2023)
12-53713798-G-A		not specified	Uncertain significance (Jul 06, 2021)
12-53713815-G-C		not specified	Uncertain significance (Aug 04, 2023)
12-53713822-C-T		not specified	Likely benign (Jul 05, 2023)
12-53713834-C-T		not specified	Uncertain significance (Aug 16, 2022)
12-53713878-G-C		not specified	Uncertain significance (Aug 02, 2021)
12-53714166-T-C		not specified	Likely benign (Dec 16, 2023)
12-53714169-C-T		not specified	Uncertain significance (Feb 28, 2023)
12-53714207-C-T		not specified	Uncertain significance (Jan 31, 2022)
12-53714224-C-T		not specified	Uncertain significance (Jul 20, 2021)
12-53714647-G-T		not specified	Uncertain significance (Jul 28, 2021)
12-53714671-C-T		not specified	Uncertain significance (Mar 13, 2023)
12-53715219-C-T		not specified	Uncertain significance (Feb 17, 2023)
12-53715229-C-T		not specified	Uncertain significance (Aug 02, 2021)
12-53715861-C-T		not specified	Likely benign (Oct 03, 2023)
12-53715902-C-T		not specified	Uncertain significance (Feb 21, 2024)
12-53715929-C-T		not specified	Uncertain significance (Jul 12, 2023)
12-53715935-C-T		not specified	Uncertain significance (Sep 14, 2021)
12-53715942-C-T		not specified	Likely benign (Aug 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALCOCO1	protein_coding	protein_coding	ENST00000550804	14	16627

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000120	1.00	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	319	381	0.838	0.0000214	4488
Missense in Polyphen		112	149.21	0.75064		1851
Synonymous	0.875	134	148	0.908	0.00000747	1359
Loss of Function	3.38	17	40.1	0.424	0.00000224	416

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000278	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.000328	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000796	0.0000791
Middle Eastern	0.000328	0.000326
South Asian	0.000471	0.000359
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a coactivator for aryl hydrocarbon and nuclear receptors (NR). Recruited to promoters through its contact with the N-terminal basic helix-loop-helix-Per-Arnt-Sim (PAS) domain of transcription factors or coactivators, such as NCOA2. During ER-activation acts synergistically in combination with other NCOA2-binding proteins, such as EP300, CREBBP and CARM1. Involved in the transcriptional activation of target genes in the Wnt/CTNNB1 pathway. Functions as a secondary coactivator in LEF1- mediated transcriptional activation via its interaction with CTNNB1. Coactivator function for nuclear receptors and LEF1/CTNNB1 involves differential utilization of two different activation regions (By similarity). In association with CCAR1 enhances GATA1- and MED1-mediated transcriptional activation from the gamma-globin promoter during erythroid differentiation of K562 erythroleukemia cells (PubMed:24245781). {ECO:0000250|UniProtKB:Q8CGU1, ECO:0000269|PubMed:24245781}.
• Pathway: Validated nuclear estrogen receptor alpha network (Consensus)

Recessive Scores

• pRec: 0.197

Intolerance Scores

• loftool: 0.757
• rvis_EVS: 0.96
• rvis_percentile_EVS: 90.15

Haploinsufficiency Scores

• pHI: 0.140
• hipred: Y
• hipred_score: 0.520
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.906

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Calcoco1

Gene ontology

• Biological process: transcription, DNA-templated;signal transduction;positive regulation of gene expression;Wnt signaling pathway;intracellular steroid hormone receptor signaling pathway;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: nuclear chromatin;nucleus;cytosol;intracellular membrane-bounded organelle
• Molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding;chromatin binding;transcription coregulator activity;transcription coactivator activity;protein binding;beta-catenin binding;protein C-terminus binding;nuclear receptor transcription coactivator activity;sequence-specific DNA binding;transcription regulatory region DNA binding;armadillo repeat domain binding