CIART
protein-codingcircadian associated repressor of transcription
Gene summary
Predicted to enable E-box binding activity. Predicted to be involved in circadian regulation of gene expression; locomotor rhythm; and negative regulation of DNA-templated transcription. Predicted to be located in PML body. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
- C1orf51
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.6 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 CIART variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_144697.4. 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 | 52 | 4 | 56 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 52 | 4 | 1 | 57 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_653298.1 | 5 | MANE Select | |
| Ensembl | ENSP00000290363.5 | 5 | MANE Select | |
| RefSeq | NP_001287767.1 | 5 | Standard | |
| RefSeq | NP_001287768.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- circadian regulation of gene expression
- locomotor rhythm
- negative regulation of transcription, DNA-templated
Molecular Function
- RNA polymerase II distal enhancer sequence-specific DNA binding
- protein binding
- E-box binding
Cellular Component
- nucleus
- PML body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000290363
- Coding exons
- 5
- Length
- 4553
- Individuals with no LoFs
- 125730
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 16
- Defined
- 125746
- p
- 0.0000636
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.00 | 179 | 221 | 0.810 | 0.0000118 | 2482 |
| Missense (PolyPhen) | 40 | 58.953 | 0.67851 | 671 | ||
| Synonymous | 1.37 | 66 | 81.8 | 0.807 | 0.00000430 | 824 |
| Loss of Function | 2.96 | 2 | 13.9 | 0.143 | 6.61e-7 | 156 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.00033 | 0.00033 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transcriptional repressor which forms a negative regulatory component of the circadian clock and acts independently of the circadian transcriptional repressors: CRY1, CRY2 and BHLHE41. In a histone deacetylase-dependent manner represses the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer. Abrogates the interaction of ARNTL/BMAL1 with the transcriptional coactivator CREBBP and can repress the histone acetyl-transferase activity of the CLOCK-ARNTL/BMAL1 heterodimer, reducing histone acetylation of its target genes. Rhythmically binds the E-box elements (5'-CACGTG-3') on circadian gene promoters and its occupancy shows circadian oscillation antiphasic to ARNTL/BMAL1. Interacts with the glucocorticoid receptor (NR3C1) and contributes to the repressive function in the glucocorticoid response (By similarity). {ECO:0000250}.;
Intolerance Scores
- RVIS EVS
- -0.25
- RVIS percentile EVS
- 35.75
Essentials
- Essential (gene trap)
- N