MYL1

myosin light chain 1, the group of Myosin light chains, class 1

Basic information

Region (hg38): 2:210290149-210315174

Links

ENSG00000168530 ∙ NCBI:4632 ∙ OMIM:160780 ∙ HGNC:7582 ∙ Uniprot:P05976 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital myopathy with reduced type 2 muscle fibers (Limited), mode of inheritance: AR
• congenital myopathy with reduced type 2 muscle fibers (Limited), mode of inheritance: AR
• congenital myopathy with reduced type 2 muscle fibers (Supportive), mode of inheritance: AR
• congenital myopathy with reduced type 2 muscle fibers (Limited), mode of inheritance: Unknown
• congenital myopathy (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital myopathy 14	AR	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	30215711

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MYL1 gene.

• not provided (18 variants)
• Inborn genetic diseases (3 variants)
• Congenital myopathy with reduced type 2 muscle fibers (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYL1 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				2		2
missense		1	4		1	6
nonsense						0
start loss					1	1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					13	13
Total	0	1	4	2	15

Variants in MYL1

This is a list of pathogenic ClinVar variants found in the MYL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-210293763-C-T		not specified	Uncertain significance (Jul 20, 2021)
2-210293791-A-C		Congenital myopathy with reduced type 2 muscle fibers	Likely pathogenic (Aug 21, 2019)
2-210293802-T-C		Congenital myopathy with reduced type 2 muscle fibers	Pathogenic (Mar 10, 2023)
2-210294124-T-A			Benign (May 22, 2021)
2-210294131-T-C			Benign (May 13, 2021)
2-210294295-C-T		not specified	Uncertain significance (Apr 28, 2023)
2-210298274-G-A			Benign (May 13, 2021)
2-210298339-TAC-T			Benign (May 13, 2021)
2-210298339-T-TAC			Benign (May 20, 2021)
2-210298339-T-TACACAC			Benign (May 16, 2021)
2-210298339-T-TACACACAC			Benign (May 14, 2021)
2-210298339-T-TACACACACAC			Benign (May 21, 2021)
2-210298474-T-G		not specified	Uncertain significance (Mar 29, 2023)
2-210298498-C-T			Uncertain significance (Jul 01, 2022)
2-210298513-T-A		not specified	Uncertain significance (Dec 18, 2023)
2-210302408-A-T			Benign (May 13, 2021)
2-210302991-C-T			Benign (May 13, 2021)
2-210303457-T-TC			Benign (May 13, 2021)
2-210303478-A-G			Benign (May 16, 2021)
2-210303543-A-G		MYL1-related disorder	Likely benign (Nov 27, 2019)
2-210303553-G-A		MYL1-related disorder	Likely benign (Dec 03, 2019)
2-210303622-A-C			Benign (May 13, 2021)
2-210314926-G-A		MYL1-related disorder	Likely benign (Jan 16, 2020)
2-210314998-C-G			Likely benign (Jan 01, 2023)
2-210314998-C-T			Likely benign (Jul 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYL1	protein_coding	protein_coding	ENST00000352451	6	25041

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000130	0.649	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.523	95	110	0.860	0.00000572	1284
Missense in Polyphen		41	35.422	1.1575		429
Synonymous	-0.504	45	40.9	1.10	0.00000237	370
Loss of Function	0.791	7	9.65	0.725	4.72e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000118	0.000118
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.000306	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory light chain of myosin. Does not bind calcium.
• Pathway: Endothelin Pathways;Association Between Physico-Chemical Features and Toxicity Associated Pathways;Striated Muscle Contraction;Regulation of Actin Cytoskeleton;G13 Signaling Pathway;Striated Muscle Contraction;Muscle contraction;Regulation of retinoblastoma protein (Consensus)

Intolerance Scores

• loftool: 0.278
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• pHI: 0.597
• hipred: N
• hipred_score: 0.400
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Myl1
• Phenotype: growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; normal 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); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: muscle contraction;muscle filament sliding;cardiac muscle contraction
• Cellular component: cytosol;muscle myosin complex;myofibril;sarcomere
• Molecular function: calcium ion binding;structural constituent of muscle