MYT1

protein-coding

myelin transcription factor 1, the group of Zinc fingers C2H2C-type

Gene summary

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]

Previous symbols:

PLPB1

MANE transcript

NM_004535.3

Inheritance

ClinVar variants

P:1U:139B:56

Top phenotype

oculoauriculovertebral spectrum with radial defects

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr20:64,102,394-64,242,253

External References & Databases

Ensembl (ENSG00000196132)

Transcript & Mutation Effects

hg38 • Region Span ~139.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

craniofacial microsomiaLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0015397

Submitter: G2P

oculoauriculovertebral spectrum with radial defectsSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007712

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MYT1 variants in ClinVar

7 Conditions Cataloged

Inborn genetic diseasesTotal: 130

MYT1-related disorderTotal: 35

not providedTotal: 32

not specifiedTotal: 27

Intellectual disabilityTotal: 4

Hereditary spastic paraplegiaTotal: 1

Autism spectrum disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004535.3. 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 clinvar	39 clinvar	4 clinvar	44
missense		1 clinvar	136 clinvar	10 clinvar	3 clinvar	150
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	1	139	49	7	196

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004535.3	RefSeq	NP_004526.1	21	MANE Select
ENST00000328439.6	Ensembl	ENSP00000327465.1	21	MANE Select
ENST00000360149.9	Ensembl	ENSP00000353269.4	14	Standard
ENST00000536311.5	Ensembl	ENSP00000442412.1	21	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
myt1b	Danio rerio	Structure: pancreatic A cell Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

myt1b

Danio rerio

Structure: pancreatic A cell

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

MECP2 and Associated Rett Syndrome
G1 to S cell cycle control
cdc25 and chk1 regulatory pathway in response to dna damage
how progesterone initiates the oocyte maturation
cell cycle: g2/m checkpoint

Biological Process

negative regulation of transcription by RNA polymerase II
regulation of transcription, DNA-templated
nervous system development
cell differentiation
positive regulation of transcription by RNA polymerase II

Molecular Function

RNA polymerase II regulatory region sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription activator activity, RNA polymerase II-specific
DNA-binding transcription factor activity
zinc ion binding

Cellular Component

nucleus
nucleoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000328439
Coding exons: 21
Length: 90461
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125748
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.56	489	677	0.723	0.0000418	7370
Missense (PolyPhen)		174	306.32	0.56803		3256
Synonymous	0.607	272	285	0.954	0.0000201	2139
Loss of Function	5.68	10	55.8	0.179	0.00000301	652

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds to the promoter region of genes encoding proteolipid proteins of the central nervous system. May play a role in the development of neurons and oligodendroglia in the CNS. May regulate a critical transition point in oligodendrocyte lineage development by modulating oligodendrocyte progenitor proliferation relative to terminal differentiation and up- regulation of myelin gene transcription. {ECO:0000269|PubMed:14962745}.;

Recessive Scores

pRec: 0.116

Intolerance Scores

LoFtool: 0.220
RVIS EVS: -1.63
RVIS percentile EVS: 2.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.988

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium