INKA1
protein-codinginka box actin regulator 1
Gene summary
Enables protein kinase binding activity and protein serine/threonine kinase inhibitor activity. Predicted to act upstream of or within neural tube development. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jul 2025]
- C3orf54
- FAM212A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~1.8 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 INKA1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_203370.2. 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 | 0 | |||||
| missense | 40 | 6 | 46 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 40 | 6 | 0 | 46 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_976248.2 | 2 | MANE Select | |
| Ensembl | ENSP00000329735.5 | 2 | MANE Select | |
| RefSeq | NP_001353210.1 | 1 | Standard | |
| Ensembl | ENSP00000563073.1 | 2 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| inka1a | Danio rerio | Structure: neurocranium Quality: decreased size abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- neural tube development
- negative regulation of protein serine/threonine kinase activity
Molecular Function
- protein binding
- protein kinase binding
- protein serine/threonine kinase inhibitor activity
Cellular Component
- nucleus
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000333323
- Coding exons
- 2
- Length
- 1777
- Individuals with no LoFs
- 125603
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 134
- Defined
- 125737
- p
- 0.000533
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.799 | 143 | 173 | 0.829 | 0.0000114 | 1822 |
| Missense (PolyPhen) | 53 | 69.361 | 0.76411 | 705 | ||
| Synonymous | 0.619 | 57 | 63.3 | 0.901 | 0.00000324 | 624 |
| Loss of Function | 0.936 | 6 | 9.03 | 0.664 | 4.76e-7 | 99 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0051 | 0.0051 | notable |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0018 | 0.0018 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000071 | 0.000070 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Inhibitor of the serine/threonine-protein kinase PAK4 (PubMed:26607847). Acts by binding PAK4 in a substrate-like manner, inhibiting the protein kinase activity (PubMed:26607847). {ECO:0000269|PubMed:26607847}.;
Intolerance Scores
- RVIS EVS
- 0.13
- RVIS percentile EVS
- 63.2
Essentials
- Essential (gene trap)
- N