MAST3
protein-codingmicrotubule associated serine/threonine kinase 3, the group of AGC family kinases|PDZ domain containing
Gene summary
Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in cytoskeleton organization and intracellular signal transduction. Predicted to be located in cytoplasm. Predicted to be active in microtubule cytoskeleton. Implicated in developmental and epileptic encephalopathy 108. [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 ~53.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0859314
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0859314
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0859314
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MAST3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001393504.1. 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 | 6 | 28 | 2 | 36 | ||
| missense | 5 | 5 | 218 | 36 | 2 | 266 |
| nonsense | 3 | 3 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 12 | 12 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 5 | 5 | 243 | 64 | 4 | 321 |
Highest pathogenic variant AF is 6.8445894e-7
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001380433.1 | 28 | MANE Select | |
| Ensembl | ENSP00000509890.1 | 28 | MANE Select | |
| RefSeq | NP_001380430.1 | 29 | Standard | |
| RefSeq | NP_001380431.1 | 28 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cytoskeleton organization
- peptidyl-serine phosphorylation
- intracellular signal transduction
Molecular Function
- magnesium ion binding
- protein serine/threonine kinase activity
- protein binding
- ATP binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000262811
- Coding exons
- 27
- Length
- 53900
- Individuals with no LoFs
- 125513
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 125526
- p
- 0.0000518
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 4.14 | 510 | 849 | 0.601 | 0.0000614 | 8281 |
| Missense (PolyPhen) | 136 | 327.66 | 0.41506 | 3149 | ||
| Synonymous | 0.857 | 346 | 367 | 0.943 | 0.0000269 | 2799 |
| Loss of Function | 5.97 | 6 | 52.8 | 0.114 | 0.00000275 | 608 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00012 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000054 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000062 | 0.000053 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.116
Intolerance Scores
- LoFtool
- 0.285
- RVIS EVS
- -1.55
- RVIS percentile EVS
- 3.31
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.818
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |