CKAP4
protein-codingcytoskeleton associated protein 4
Gene summary
Enables RNA binding activity. Located in lipid droplet and rough endoplasmic reticulum. Biomarker of hepatocellular carcinoma. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~66.4 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 CKAP4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006825.4. 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 | 2 | 2 | 4 | |||
| missense | 75 | 6 | 1 | 82 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 75 | 8 | 3 | 86 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006816.2 | 2 | MANE Select | |
| Ensembl | ENSP00000367265.4 | 2 | MANE Select | |
| Ensembl | ENSP00000449240.1 | 2 | Standard | |
| Ensembl | ENSP00000550674.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Protein processing in endoplasmic reticulum - Homo sapiens (human)
- Neutrophil degranulation
- Post-translational protein phosphorylation
- Post-translational protein modification
- Surfactant metabolism
Biological Process
- neutrophil degranulation
- post-translational protein modification
- cellular protein metabolic process
Molecular Function
- RNA binding
Cellular Component
- endoplasmic reticulum
- endoplasmic reticulum lumen
- endoplasmic reticulum membrane
- rough endoplasmic reticulum
- lipid droplet
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000378026
- Coding exons
- 2
- Length
- 66403
- Individuals with no LoFs
- 125737
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 11
- Defined
- 125748
- p
- 0.0000437
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.852 | 249 | 290 | 0.859 | 0.0000182 | 3857 |
| Missense (PolyPhen) | 85 | 112.63 | 0.75471 | 1364 | ||
| Synonymous | -0.417 | 142 | 136 | 1.05 | 0.00000913 | 1213 |
| Loss of Function | 2.85 | 3 | 14.9 | 0.202 | 6.46e-7 | 204 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: High-affinity epithelial cell surface receptor for APF.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- LoFtool
- 0.282
- RVIS EVS
- -0.91
- RVIS percentile EVS
- 10.03
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.608
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |