MYT1

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

Basic information

Region (hg38): 20:64102393-64242253

Previous symbols: [ "PLPB1" ]

Links

ENSG00000196132 ∙ NCBI:4661 ∙ OMIM:600379 ∙ HGNC:7622 ∙ Uniprot:Q01538 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (53 variants)
• not provided (32 variants)
• Intellectual disability (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				15	6	21
missense		1	36	4	2	43
nonsense						0
start loss						0
frameshift						0
inframe indel				1	1	2
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding			16	1	1	18
Total	0	1	52	21	10

Variants in MYT1

This is a list of pathogenic ClinVar variants found in the MYT1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-64105883-C-T		not specified	Uncertain significance (Feb 06, 2024)
20-64105931-T-C		not specified	Uncertain significance (Apr 07, 2022)
20-64105945-C-T		not specified	Uncertain significance (Apr 28, 2022)
20-64105952-C-T		not specified	Uncertain significance (Oct 12, 2021)
20-64105975-G-A		not specified	Uncertain significance (Dec 18, 2023)
20-64105988-C-T		not specified	Uncertain significance (Aug 11, 2022)
20-64106011-G-A		not specified	Uncertain significance (Mar 16, 2022)
20-64106039-C-T		not specified	Uncertain significance (Jan 26, 2022)
20-64106113-C-T		not specified	Uncertain significance (Dec 19, 2023)
20-64106129-G-A		not specified	Uncertain significance (Sep 14, 2023)
20-64106130-G-T		not specified	Uncertain significance (Feb 26, 2024)
20-64106158-A-G		not specified	Uncertain significance (Dec 12, 2023)
20-64106222-G-A		not specified	Uncertain significance (Aug 10, 2021)
20-64106233-C-T		not specified	Uncertain significance (Jul 06, 2021)
20-64106260-T-C		not specified	Uncertain significance (Apr 20, 2023)
20-64106348-C-T		not specified	Uncertain significance (Sep 01, 2021)
20-64106351-G-A		not specified	Uncertain significance (Jan 23, 2024)
20-64106432-A-G		not specified	Uncertain significance (Nov 18, 2022)
20-64106465-C-T		not specified	Likely benign (Jul 15, 2021)
20-64106542-A-T		not specified	Uncertain significance (May 18, 2023)
20-64106548-G-A		not specified	Uncertain significance (Sep 01, 2021)
20-64106641-G-A		not specified	Uncertain significance (Oct 17, 2023)
20-64106672-C-T		not specified	Uncertain significance (Mar 29, 2023)
20-64106681-C-T		not specified	Uncertain significance (Jun 29, 2023)
20-64106713-G-A		not specified	Uncertain significance (Mar 08, 2024)

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