MZT2A
protein-codingmitotic spindle organizing protein 2A, the group of MicroRNA protein coding host genes
Gene summary
Predicted to be involved in microtubule nucleation. Located in centrosome. [provided by Alliance of Genome Resources, Jun 2026]
- FAM128A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~27.8 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 MZT2A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001085365.2. 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 | 41 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 42 | 0 | 0 | 42 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001078834.1 | 3 | MANE Select | |
| Ensembl | ENSP00000311500.6 | 3 | MANE Select | |
| Ensembl | ENSP00000403353.1 | 4 | Standard | |
| Ensembl | ENSP00000556612.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Recruitment of mitotic centrosome proteins and complexes
- Centrosome maturation
- G2/M Transition
- Mitotic G2-G2/M phases
- Recruitment of NuMA to mitotic centrosomes
Cellular Component
- nucleoplasm
- centrosome
- spindle
- cytosol
- gamma-tubulin ring complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000309451
- Coding exons
- 3
- Length
- 27844
- Individuals with no LoFs
- 125013
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 125018
- p
- 0.0000200
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.301 | 93 | 85.2 | 1.09 | 0.00000465 | 978 |
| Missense (PolyPhen) | 28 | 24.991 | 1.1204 | 327 | ||
| Synonymous | -0.515 | 45 | 40.8 | 1.10 | 0.00000248 | 350 |
| Loss of Function | -1.69 | 6 | 2.89 | 2.07 | 1.23e-7 | 43 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000063 | 0.000062 | rare |
| Latino/Admixed American | 0.000062 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000020 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |