MYT1

Chr 20

myelin transcription factor 1

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

NCBI Gene: 4661 ENSG00000196132 UniProt: Q01538 OMIM: 600379

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.

OMIM ResearchSummary from RefSeq, UniProt

The protein encoded by this gene is a member of a family of neural specific, zinc finger-containing DNA-binding proteins. The protein binds to the promoter regions of proteolipid proteins of the central nervous system and plays a role in the developing nervous system. [provided by RefSeq, Jul 2008]

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.30

Clinical Summary— MYT1

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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.

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ClinVar Variants

1 unique Pathogenic / Likely Pathogenic· 124 VUS of 195 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 OE?0.18 (0.11–0.30)

0≤0.351.4

Missense OE?0.72 (0.67–0.78)

0≤0.61.4

Synonymous OE?0.95

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

This gene — mechanism propensity

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

195 submitted variants in ClinVar

ClinVar

Classification Summary

Likely Pathogenic1

VUS124

Likely Benign42

Benign15

Likely Pathogenic

124

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	1	0	0	1
VUS	124	0	0	124
Likely Benign	11	3	28	42
Benign	4	2	9	15
Total	140	5	37	182

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

View in ClinVar →

36 pathogenic / likely-pathogenic (of 54) ClinVar copy-number / structural variants overlap MYT1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →