CARF
protein-codingcalcium responsive transcription factor
Gene summary
Enables DNA binding activity and DNA-binding transcription activator activity, RNA polymerase II-specific. Involved in cellular response to calcium ion. Predicted to be located in granular component. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
- ALS2CR8
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~76.0 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 CARF variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024744.17. 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 | 3 | 2 | 5 | |||
| missense | 92 | 10 | 2 | 104 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 97 | 11 | 4 | 112 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_079020.13 | 14 | MANE Select | |
| Ensembl | ENSP00000414644.1 | 14 | MANE Select | |
| RefSeq | NP_001098056.1 | 14 | Standard | |
| RefSeq | NP_001269839.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cellular response to potassium ion
- positive regulation of transcription from RNA polymerase II promoter in response to calcium ion
- cellular response to calcium ion
Molecular Function
- RNA polymerase II proximal promoter sequence-specific DNA binding
- DNA-binding transcription activator activity, RNA polymerase II-specific
- DNA binding
- DNA-binding transcription factor activity
Cellular Component
- nucleus
- nucleoplasm
- nucleolus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000402905
- Coding exons
- 14
- Length
- 74850
- Individuals with no LoFs
- 124750
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 43
- Defined
- 124793
- p
- 0.000172
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.25 | 311 | 379 | 0.820 | 0.0000184 | 4735 |
| Missense (PolyPhen) | 79 | 114.75 | 0.68846 | 1497 | ||
| Synonymous | 0.810 | 116 | 128 | 0.909 | 0.00000579 | 1393 |
| Loss of Function | 2.93 | 16 | 34.6 | 0.463 | 0.00000147 | 443 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000065 | rare |
| Latino/Admixed American | 0.00071 | 0.00067 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000097 | 0.000097 | rare |
| South Asian | 0.00014 | 0.00013 | rare |
| Other | 0.00051 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acts as a transcriptional activator that mediates the calcium- and neuron-selective induction of BDNF exon III transcription. Binds to the consensus calcium-response element CaRE1 5'-CTATTTCGAG-3' sequence. {ECO:0000269|PubMed:11832226, ECO:0000269|PubMed:22174809}.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- RVIS EVS
- 0.16
- RVIS percentile EVS
- 64.82
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |