MYO1D

myosin ID, the group of Protein phosphatase 1 regulatory subunits|Myosin heavy chains, class I

Basic information

Region (hg38): 17:32492522-32877177

Links

ENSG00000176658 ∙ NCBI:4642 ∙ OMIM:606539 ∙ HGNC:7598 ∙ Uniprot:O94832 ∙ 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 MYO1D gene.

• not_specified (123 variants)
• not_provided (12 variants)
• Preeclampsia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYO1D gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015194.3. 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				3	3	6
missense			120	4	1	125
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	120	7	4

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYO1D	protein_coding	protein_coding	ENST00000318217	22	384656

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.28e-12	1.00	125655	0	93	125748	0.000370

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.36	487	579	0.841	0.0000344	6652
Missense in Polyphen		159	216.13	0.73567		2502
Synonymous	0.109	207	209	0.990	0.0000123	1870
Loss of Function	3.36	29	56.2	0.516	0.00000329	638

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000867	0.000867
Ashkenazi Jewish	0.000398	0.000397
East Asian	0.000383	0.000381
Finnish	0.000417	0.000416
European (Non-Finnish)	0.000354	0.000343
Middle Eastern	0.000383	0.000381
South Asian	0.000301	0.000294
Other	0.000498	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Myosins are actin-based motor molecules with ATPase activity. Unconventional myosins serve in intracellular movements. Their highly divergent tails are presumed to bind to membranous compartments, which would be moved relative to actin filaments (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.154

Intolerance Scores

• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.71

Haploinsufficiency Scores

• pHI: 0.888
• hipred: Y
• hipred_score: 0.706
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.922

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Myo1d

Gene ontology

• Biological process: negative regulation of phosphatase activity;forebrain development;cellular localization;early endosome to recycling endosome transport
• Cellular component: endosome;smooth endoplasmic reticulum;cytosol;brush border;basolateral plasma membrane;myosin complex;axon;axolemma;cytoplasmic vesicle;neuron projection;neuronal cell body;myelin sheath;plasma membrane raft;extracellular exosome;apical dendrite
• Molecular function: microfilament motor activity;calmodulin binding;ATP binding;protein domain specific binding;actin-dependent ATPase activity;calcium-dependent protein binding;actin filament binding