MYL9

myosin light chain 9, the group of Myosin light chains, class 2

Basic information

Region (hg38): 20:36541497-36551447

Links

ENSG00000101335

∙ NCBI:10398 ∙ OMIM:609905 ∙ HGNC:15754 ∙ Uniprot:P24844 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

megacystis-microcolon-intestinal hypoperistalsis syndrome 4 (Strong), mode of inheritance: AR
megacystis-microcolon-intestinal hypoperistalsis syndrome 4 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Megacystis-microcolon-intestinal hypoperistalsis syndrome 4	AR	Gastrointestinal; Renal	Individuals have been described as benefiting from surgical interventions, including related to renal anomalies and nephrolithiasis; Multivisceral transplantation has been described	Gastrointestinal; Genitourinary; Musculoskeletal; Ophthalmologic; Renal	27481187; 29453416; 33031641

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MYL9 gene.

not_specified (18 variants)
not_provided (1 variants)
Megacystis-microcolon-intestinal_hypoperistalsis_syndrome_4 (1 variants)
Visceral_myopathy_1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYL9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006097.5. 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						0
missense			18 clinvar			18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	0	1	18	0	0

Highest pathogenic variant AF is 0.000008210866

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYL9	protein_coding	protein_coding	ENST00000279022	3	8342

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0198	0.757	125728	0	18	125746	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	83	119	0.698	0.00000773	1176
Missense in Polyphen		17	30.866	0.55077		364
Synonymous	0.375	43	46.2	0.930	0.00000332	301
Loss of Function	0.841	3	5.04	0.596	2.13e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000146	0.000146
Ashkenazi Jewish	0.00	0.00
East Asian	0.000277	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000711	0.0000703
Middle Eastern	0.000277	0.000272
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Myosin regulatory subunit that plays an important role in regulation of both smooth muscle and nonmuscle cell contractile activity via its phosphorylation. Implicated in cytokinesis, receptor capping, and cell locomotion. {ECO:0000269|PubMed:11942626, ECO:0000269|PubMed:2526655}.;
Pathway: Focal adhesion - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Tight junction - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Focal Adhesion;Striated Muscle Contraction;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;Developmental Biology;Smooth Muscle Contraction;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;EPH-Ephrin signaling;EPHA-mediated growth cone collapse;RHO GTPases Activate ROCKs;RHO GTPases activate PAKs;RHO GTPases activate PKNs;RHO GTPases activate CIT;Muscle contraction;RHO GTPase Effectors;Signaling by Rho GTPases;Sema4D induced cell migration and growth-cone collapse;Sema4D in semaphorin signaling;Semaphorin interactions;Axon guidance;Integrin-linked kinase signaling;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

pRec: 0.149

Intolerance Scores

loftool: 0.626
rvis_EVS: -0.16
rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

pHI: 0.284
hipred: N
hipred_score: 0.455
ghis: 0.646

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.982

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Myl9
Phenotype

Gene ontology

Biological process: muscle contraction;regulation of muscle contraction;regulation of megakaryocyte differentiation;platelet aggregation
Cellular component: stress fiber;cytosol;muscle myosin complex;Z disc
Molecular function: calcium ion binding;structural constituent of muscle;myosin heavy chain binding