CACTIN
protein-codingcactin, spliceosome C complex subunit, the group of Spliceosomal C complex|Spliceosomal P complex
Gene summary
Enables RNA binding activity. Involved in several processes, including cellular response to cytokine stimulus; negative regulation of cytokine production; and negative regulation of signal transduction. Located in nuclear speck. Part of catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Jun 2026]
- C19orf29
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.2 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 CACTIN variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001080543.2. 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 | 1 | 4 | |||
| missense | 83 | 5 | 88 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 87 | 6 | 0 | 93 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001074012.1 | 10 | MANE Select | |
| Ensembl | ENSP00000415078.1 | 10 | MANE Select | |
| RefSeq | NP_067054.1 | 10 | Standard | |
| Ensembl | ENSP00000221899.4 | 10 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| cactin | Danio rerio | Structure: photoreceptor outer segment layer Quality: disheveled abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- mRNA splicing, via spliceosome
- negative regulation of protein phosphorylation
- multicellular organism development
- negative regulation of lipopolysaccharide-mediated signaling pathway
- negative regulation of NF-kappaB transcription factor activity
Molecular Function
- RNA binding
- protein binding
Cellular Component
- nucleus
- nucleoplasm
- cytosol
- nuclear speck
- catalytic step 2 spliceosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000429344
- Coding exons
- 10
- Length
- 16175
- Individuals with no LoFs
- 124434
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 124436
- p
- 0.00000804
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.20 | 315 | 521 | 0.605 | 0.0000401 | 4820 |
| Missense (PolyPhen) | 90 | 208.43 | 0.4318 | 1836 | ||
| Synonymous | -1.37 | 257 | 231 | 1.11 | 0.0000186 | 1446 |
| Loss of Function | 5.31 | 1 | 34.8 | 0.0288 | 0.00000168 | 378 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000089 | 0.0000089 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in the regulation of innate immune response. Acts as negative regulator of Toll-like receptor and interferon- regulatory factor (IRF) signaling pathways. Contributes to the regulation of transcriptional activation of NF-kappa-B target genes in response to endogenous proinflammatory stimuli. May play a role during early embryonic development. Probably involved in pre-mRNA splicing. {ECO:0000269|PubMed:20829348}.;
Intolerance Scores
- RVIS EVS
- -0.75
- RVIS percentile EVS
- 13.67
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- H
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |