SLAIN2
protein-codingSLAIN motif family member 2
Gene summary
Involved in cytoplasmic microtubule organization; microtubule nucleation; and positive regulation of microtubule polymerization. Located in ciliary tip; cytosol; and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Jun 2026]
- KIAA1458
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~84.7 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 SLAIN2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020846.2. 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 | 1 | 1 | 2 | |||
| missense | 101 | 2 | 103 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 104 | 2 | 1 | 107 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_065897.1 | 8 | MANE Select | |
| Ensembl | ENSP00000264313.5 | 8 | MANE Select | |
| Ensembl | ENSP00000426744.1 | 3 | Standard | |
| Ensembl | ENSP00000424473.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- microtubule nucleation
- positive regulation of microtubule polymerization
- cytoplasmic microtubule organization
Molecular Function
- protein binding
Cellular Component
- centrosome
- cytosol
- microtubule cytoskeleton
- microtubule plus-end
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000264313
- Coding exons
- 8
- Length
- 84891
- Individuals with no LoFs
- 124624
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 15
- Defined
- 124639
- p
- 0.0000602
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.720 | 258 | 293 | 0.882 | 0.0000159 | 3706 |
| Missense (PolyPhen) | 96 | 147.55 | 0.65064 | 1699 | ||
| Synonymous | 0.479 | 96 | 102 | 0.940 | 0.00000501 | 1202 |
| Loss of Function | 3.65 | 4 | 22.8 | 0.176 | 0.00000129 | 287 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0.000093 | 0.000093 | rare |
| European (Non-Finnish) | 0.000045 | 0.000044 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Binds to the plus end of microtubules and regulates microtubule dynamics and microtubule organization. Promotes cytoplasmic microtubule nucleation and elongation. Required for normal structure of the microtubule cytoskeleton during interphase. {ECO:0000269|PubMed:21646404}.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- LoFtool
- 0.308
- RVIS EVS
- -0.29
- RVIS percentile EVS
- 32.94
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- H
- Indispensability pred.
- E
- Indispensability score
- 0.693
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |