MYF6

myogenic factor 6, the group of Basic helix-loop-helix proteins|Myogenic regulatory family

Basic information

Region (hg38): 12:80707633-80709474

Links

ENSG00000111046 ∙ NCBI:4618 ∙ OMIM:159991 ∙ HGNC:7566 ∙ Uniprot:P23409 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Myopathy, centronuclear, 3	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal	11053684

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MYF6 gene.

• Autosomal dominant centronuclear myopathy (39 variants)
• Centronuclear Myopathy, Dominant (13 variants)
• not provided (10 variants)
• Inborn genetic diseases (5 variants)
• not specified (4 variants)
• MYF6-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYF6 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				7	1	8
missense		1	27	3	1	32
nonsense			2			2
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			1			1
non coding			4	2	3	9
Total	0	1	35	12	5

Variants in MYF6

This is a list of pathogenic ClinVar variants found in the MYF6 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-80707736-T-G		Autosomal dominant centronuclear myopathy	Uncertain significance (Jul 05, 2022)
12-80707765-G-A		Autosomal dominant centronuclear myopathy	Uncertain significance (May 01, 2017)
12-80707769-G-A		Centronuclear Myopathy, Dominant	Uncertain significance (Jun 14, 2016)
12-80707798-G-A		Autosomal dominant centronuclear myopathy • not specified	Conflicting classifications of pathogenicity (Jun 19, 2023)
12-80707810-T-C		Autosomal dominant centronuclear myopathy	Uncertain significance (Jun 20, 2022)
12-80707823-C-T		Autosomal dominant centronuclear myopathy	Uncertain significance (Dec 29, 2020)
12-80707854-G-A		not specified	Likely benign (-)
12-80707864-C-G		Autosomal dominant centronuclear myopathy	Uncertain significance (Sep 01, 2022)
12-80707891-G-A		Centronuclear Myopathy, Dominant • Autosomal dominant centronuclear myopathy	Conflicting classifications of pathogenicity (Jan 09, 2023)
12-80707895-A-T		Autosomal dominant centronuclear myopathy	Uncertain significance (Oct 25, 2022)
12-80707902-T-G		Autosomal dominant centronuclear myopathy	Uncertain significance (Feb 04, 2022)
12-80707903-G-A		Autosomal dominant centronuclear myopathy	Uncertain significance (Jan 15, 2024)
12-80707912-C-T		Autosomal dominant centronuclear myopathy	Uncertain significance (Aug 09, 2022)
12-80707939-C-T		Autosomal dominant centronuclear myopathy • not specified	Uncertain significance (Dec 18, 2023)
12-80707987-G-GC		Autosomal dominant centronuclear myopathy	Uncertain significance (Nov 08, 2022)
12-80707988-C-A		Autosomal dominant centronuclear myopathy	Benign/Likely benign (Nov 27, 2023)
12-80707999-C-T		Autosomal dominant centronuclear myopathy	Uncertain significance (Mar 09, 2022)
12-80708000-G-A		Centronuclear Myopathy, Dominant • Autosomal dominant centronuclear myopathy	Uncertain significance (Apr 30, 2020)
12-80708007-A-T		Autosomal dominant centronuclear myopathy	Uncertain significance (Jul 13, 2021)
12-80708011-G-T		Autosomal dominant centronuclear myopathy	Benign (Sep 08, 2020)
12-80708013-C-T		Autosomal dominant centronuclear myopathy	Likely benign (Jun 21, 2018)
12-80708050-G-C		Autosomal dominant centronuclear myopathy	Uncertain significance (Aug 21, 2018)
12-80708053-G-T		Autosomal dominant centronuclear myopathy • MYF6-related disorder	Conflicting classifications of pathogenicity (Apr 24, 2023)
12-80708059-G-T		not specified	Uncertain significance (May 04, 2022)
12-80708066-T-C		Autosomal dominant centronuclear myopathy	Likely benign (Oct 03, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYF6	protein_coding	protein_coding	ENST00000228641	3	1977

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00412	0.873	125687	1	60	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.362	147	135	1.09	0.00000745	1570
Missense in Polyphen		78	69.829	1.117		823
Synonymous	0.524	52	57.0	0.912	0.00000318	494
Loss of Function	1.30	5	9.28	0.539	5.01e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000821	0.000821
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000211	0.000211
Middle Eastern	0.000163	0.000163
South Asian	0.000359	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in muscle differentiation (myogenic factor). Induces fibroblasts to differentiate into myoblasts. Probable sequence specific DNA-binding protein.
• Pathway: Exercise-induced Circadian Regulation;Developmental Biology;CDO in myogenesis;Myogenesis;C-MYB transcription factor network (Consensus)

Recessive Scores

• pRec: 0.281

Intolerance Scores

• loftool: 0.466
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.901
• hipred: Y
• hipred_score: 0.662
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Myf6
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; muscle phenotype; vision/eye 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); normal phenotype; neoplasm; embryo phenotype; respiratory system phenotype; skeleton phenotype

Zebrafish Information Network

• Gene name: myf6
• Affected structure: primary motor neuron
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: somitogenesis;regulation of transcription by RNA polymerase II;skeletal muscle tissue development;skeletal muscle cell differentiation;muscle cell fate commitment;skeletal muscle tissue regeneration;positive regulation of myoblast differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of skeletal muscle fiber development;positive regulation of muscle cell differentiation;muscle tissue morphogenesis;positive regulation of myoblast fusion
• Cellular component: nucleus;nucleoplasm;RNA polymerase II transcription factor complex
• Molecular function: RNA polymerase II proximal promoter 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;protein heterodimerization activity;E-box binding