CALCOCO1
protein-codingcalcium binding and coiled-coil domain 1
Gene summary
Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; beta-catenin binding activity; and transcription coactivator activity. Involved in positive regulation of DNA-templated transcription and positive regulation of gene expression. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~19.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CALCOCO1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020898.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 95 | 6 | 101 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 100 | 7 | 0 | 107 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_065949.1 | 14 | MANE Select | |
| Ensembl | ENSP00000449960.1 | 14 | MANE Select | |
| RefSeq | NP_001137154.1 | 13 | Standard | |
| Ensembl | ENSP00000262059.4 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Validated nuclear estrogen receptor alpha network
Biological Process
- transcription, DNA-templated
- signal transduction
- positive regulation of gene expression
- Wnt signaling pathway
- intracellular steroid hormone receptor signaling pathway
Molecular Function
- RNA polymerase II distal enhancer sequence-specific DNA binding
- chromatin binding
- transcription coregulator activity
- transcription coactivator activity
- protein binding
Cellular Component
- nuclear chromatin
- nucleus
- cytosol
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000550804
- Coding exons
- 14
- Length
- 16627
- Individuals with no LoFs
- 125715
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 33
- Defined
- 125748
- p
- 0.000131
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.12 | 319 | 381 | 0.838 | 0.0000214 | 4488 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000080 | 0.000079 | rare |
| South Asian | 0.00047 | 0.00036 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.197
Intolerance Scores
- LoFtool
- 0.757
- RVIS EVS
- 0.96
- RVIS percentile EVS
- 90.15
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.906
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |