MYL5

myosin light chain 5, the group of Myosin light chains, class 2

Basic information

Region (hg38): 4:673580-682028

Links

ENSG00000215375 ∙ NCBI:4636 ∙ OMIM:160782 ∙ HGNC:7586 ∙ Uniprot:Q02045 ∙ 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 MYL5 gene.

• not_specified (36 variants)
• Retinitis_pigmentosa_40 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYL5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002477.2. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			36			36
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	36	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYL5	protein_coding	protein_coding	ENST00000400159	7	8454

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.40e-14	0.00140	125200	1	259	125460	0.00104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.586	114	97.7	1.17	0.00000559	1147
Missense in Polyphen		33	25.101	1.3147		320
Synonymous	-1.84	55	40.1	1.37	0.00000309	286
Loss of Function	-2.09	16	9.17	1.74	4.72e-7	111

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00769	0.00752
Ashkenazi Jewish	0.00	0.00
East Asian	0.00457	0.00444
Finnish	0.00	0.00
European (Non-Finnish)	0.000259	0.000255
Middle Eastern	0.00457	0.00444
South Asian	0.000327	0.000327
Other	0.000824	0.000818

dbNSFP

Source: dbNSFP

• Pathway: Focal adhesion - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Focal Adhesion;Smooth Muscle Contraction;Muscle contraction (Consensus)

Intolerance Scores

• loftool: 0.677
• rvis_EVS: 1.37
• rvis_percentile_EVS: 94.49

Haploinsufficiency Scores

• pHI: 0.208
• hipred: N
• hipred_score: 0.170
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.762

Gene Damage Prediction

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

Gene ontology

• Biological process: muscle contraction;regulation of muscle contraction
• Cellular component: cytosol;muscle myosin complex
• Molecular function: calcium ion binding;structural constituent of muscle