MYT1

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

Basic information

Region (hg38): 20:64102394-64242253

Previous symbols: [ "PLPB1" ]

Links

ENSG00000196132

∙ NCBI:4661 ∙ OMIM:600379 ∙ HGNC:7622 ∙ Uniprot:Q01538 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

craniofacial microsomia (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MYT1 gene.

Inborn_genetic_diseases (112 variants)
MYT1-related_disorder (33 variants)
not_provided (30 variants)
Intellectual_disability (4 variants)
Hereditary_spastic_paraplegia (1 variants)
Autism_spectrum_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004535.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				28 clinvar	5 clinvar	33
missense		1 clinvar	112 clinvar	10 clinvar	3 clinvar	126
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	112	38	8

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYT1	protein_coding	protein_coding	ENST00000328439	21	90461

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.978	0.0221	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.56	489	677	0.723	0.0000418	7370
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000370	0.000366
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000623	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

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}.;
Pathway: 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;rb tumor suppressor/checkpoint signaling in response to dna damage (Consensus)

Recessive Scores

pRec: 0.116

Intolerance Scores

loftool: 0.220
rvis_EVS: -1.63
rvis_percentile_EVS: 2.85

Haploinsufficiency Scores

pHI: 0.938
hipred: Y
hipred_score: 0.755
ghis: 0.625

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Myt1
Phenotype: muscle phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Zebrafish Information Network

Gene name: myt1b
Affected structure: pancreatic A cell
Phenotype tag: abnormal
Phenotype quality: decreased amount

Gene ontology

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
Cellular component: nucleus;nucleoplasm;cytosol
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