MYT1

Chr 20

myelin transcription factor 1

Also known as: C20orf36, MTF1, MYTI, NZF2, PLPB1, ZC2H2C1, ZC2HC4A

NCBI Gene: 4661ENSG00000196132UniProt: Q01538

The MYT1 protein is a zinc finger DNA-binding transcription factor that binds to promoter regions of central nervous system proteolipid protein genes and regulates oligodendrocyte development and myelin gene transcription. Mutations cause autosomal dominant intellectual disability with variable features that may include seizures, autism spectrum disorder, and developmental delays, typically with onset in early childhood. This gene is highly constrained against loss-of-function variants in the general population.

Summary from RefSeq, UniProt
Research Assistant →
LOFmechanismLOEUF 0.30
Clinical Summary— MYT1
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.98). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
37 unique Pathogenic / Likely Pathogenic· 139 VUS of 249 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.30LOEUF
pLI 0.978
Z-score 5.68
OE 0.18 (0.11–0.30)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
2.56Z-score
OE missense 0.72 (0.67–0.78)
489 obs / 676.6 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.18 (0.11–0.30)
0≤0.351.4
Missense OE0.72 (0.67–0.78)
0≤0.61.4
Synonymous OE0.95
0≤1.21.6
LoF obs/exp: 10 / 55.8Missense obs/exp: 489 / 676.6Syn Z: 0.61
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
limitedMYT1-related oculo-auriculo-vertebral spectrum (OAVS) (Goldenhar syndrome)LOFAD
DN
0.2997th %ile
GOF
0.2597th %ile
LOF
0.79top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.30

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

249 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic30
Likely Pathogenic7
VUS139
Likely Benign43
Benign17
30
Pathogenic
7
Likely Pathogenic
139
VUS
43
Likely Benign
17
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
30
0
30
Likely Pathogenic
0
1
6
0
7
VUS
0
124
15
0
139
Likely Benign
0
11
4
28
43
Benign
0
4
4
9
17
Total01405937236

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

MYT1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 4 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients