KATNBL1
protein-codingkatanin regulatory subunit B1 like 1
Gene summary
Predicted to enable microtubule binding activity. Involved in cytoplasmic microtubule organization and positive regulation of cytoskeleton organization. Located in mitotic spindle pole; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
- C15orf29
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~69.4 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 KATNBL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024713.3. 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 | 50 | 1 | 51 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 53 | 1 | 0 | 54 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_078989.1 | 9 | MANE Select | |
| Ensembl | ENSP00000256544.3 | 9 | MANE Select | |
| Ensembl | ENSP00000452963.1 | 4 | Standard | |
| Ensembl | ENSP00000454010.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- positive regulation of cytoskeleton organization
Molecular Function
- protein binding
Cellular Component
- nucleus
- nucleolus
- cytoplasm
- mitotic spindle pole
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000256544
- Coding exons
- 9
- Length
- 69423
- Individuals with no LoFs
- 125730
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 11
- Defined
- 125741
- p
- 0.0000437
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.731 | 122 | 147 | 0.830 | 0.00000688 | 1995 |
| Missense (PolyPhen) | 33 | 47.538 | 0.69418 | 700 | ||
| Synonymous | 2.15 | 30 | 49.2 | 0.610 | 0.00000219 | 534 |
| Loss of Function | 3.20 | 3 | 17.4 | 0.173 | 7.97e-7 | 238 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000089 | 0.000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulates microtubule-severing activity of KATNAL1 in a concentration-dependent manner in vitro. {ECO:0000269|PubMed:26929214}.;
Recessive Scores
- pRec
- 0.101
Intolerance Scores
- RVIS EVS
- 0.13
- RVIS percentile EVS
- 62.74
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 |