MYL12A

myosin light chain 12A, the group of Myosin light chains, class 2

Basic information

Region (hg38): 18:3247481-3256236

Links

ENSG00000101608 ∙ NCBI:10627 ∙ ∙ HGNC:16701 ∙ Uniprot:P19105 ∙ 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 MYL12A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYL12A 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					1	1
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	1

Variants in MYL12A

This is a list of pathogenic ClinVar variants found in the MYL12A region.

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

Position	Type	Phenotype	Significance	ClinVar
18-3253252-C-G		not specified	Uncertain significance (Jan 09, 2024)
18-3253293-C-T		not specified	Uncertain significance (Oct 20, 2024)
18-3253317-A-G		not specified	Uncertain significance (Dec 02, 2022)
18-3253353-G-A		not specified	Uncertain significance (Aug 13, 2021)
18-3253900-A-G		not specified	Uncertain significance (Feb 01, 2025)
18-3253942-C-T		not specified	Uncertain significance (Apr 20, 2024)
18-3253944-C-T			Benign (May 08, 2017)
18-3253999-C-T		not specified	Uncertain significance (Mar 16, 2022)
18-3255904-G-A		not specified	Uncertain significance (Jan 08, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYL12A	protein_coding	protein_coding	ENST00000217652	3	8756

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000512	0.466	125726	0	17	125743	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.48	56	96.9	0.578	0.00000498	1165
Missense in Polyphen		6	15.674	0.3828		206
Synonymous	0.502	29	32.6	0.888	0.00000160	290
Loss of Function	0.152	5	5.38	0.929	2.24e-7	77

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000618	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000328	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000531	0.0000527
Middle Eastern	0.000328	0.000326
South Asian	0.000131	0.000131
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 (By similarity). {ECO:0000250}.
• Pathway: Platelet activation - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Tight junction - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Focal Adhesion;Developmental Biology;Smooth Muscle Contraction;EPH-Ephrin signaling;Ephrin signaling;Muscle contraction;Axon guidance (Consensus)

Intolerance Scores

• loftool: 0.782
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.506
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.948

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Myl12a

Gene ontology

• Biological process: muscle contraction;platelet aggregation
• Cellular component: cytosol;myosin complex;extracellular exosome
• Molecular function: calcium ion binding;protein binding