MYO1E

myosin IE, the group of Myosin heavy chains, class I|MicroRNA protein coding host genes

Basic information

Region (hg38): 15:59132433-59372871

Links

ENSG00000157483 ∙ NCBI:4643 ∙ OMIM:601479 ∙ HGNC:7599 ∙ Uniprot:Q12965 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• focal segmental glomerulosclerosis 6 (Strong), mode of inheritance: AR
• focal segmental glomerulosclerosis 6 (Strong), mode of inheritance: AR
• familial idiopathic steroid-resistant nephrotic syndrome (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Focal segmental glomerulosclerosis 6	AR	Renal	The condition can involve early-onset renal disease, and awareness may allow prompt diagnosis and management (eg, glucocorticoid and cyclosporine use has been descvribed as beneficial); Renal transplant has been described	Renal	21756023

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MYO1E gene.

• not provided (339 variants)
• Inborn genetic diseases (71 variants)
• Focal segmental glomerulosclerosis 6 (70 variants)
• not specified (7 variants)
• Kidney disorder (6 variants)
• MYO1E-related condition (1 variants)
• Nephrotic syndrome (1 variants)
• Microscopic hematuria (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYO1E 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			4	44	6	54
missense		1	121	7		129
nonsense	4		1			5
start loss						0
frameshift		1				1
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1					1
splice region			6	11	4	21
non coding			23	70	92	185
Total	5	2	150	121	98

Variants in MYO1E

This is a list of pathogenic ClinVar variants found in the MYO1E region.

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

Position	Type	Phenotype	Significance	ClinVar
15-59136664-T-C		Kidney disorder	Likely benign (Jan 16, 2017)
15-59137272-T-G			Benign (Dec 29, 2019)
15-59137339-C-T			Likely benign (May 05, 2020)
15-59137366-G-C		Kidney disorder	Benign/Likely benign (Feb 15, 2020)
15-59137399-T-C		Inborn genetic diseases	Uncertain significance (Oct 03, 2023)
15-59137407-G-A			Uncertain significance (Apr 07, 2017)
15-59137426-C-A			Uncertain significance (Dec 02, 2023)
15-59137427-G-A			Uncertain significance (Oct 02, 2021)
15-59137432-C-T			Uncertain significance (Apr 02, 2022)
15-59137438-G-A		Inborn genetic diseases	Uncertain significance (Jul 19, 2022)
15-59137459-G-A		MYO1E-related disorder	Likely benign (Dec 20, 2022)
15-59137464-G-C			Benign (Feb 22, 2023)
15-59137741-G-C			Benign (Nov 12, 2018)
15-59137959-G-A			Benign (Nov 12, 2018)
15-59138114-C-A			Benign (Feb 15, 2020)
15-59138171-GTCCCAGCC-G			Likely benign (Jul 19, 2022)
15-59138180-AAC-GGA			Uncertain significance (Jul 16, 2022)
15-59138186-C-G			Likely benign (Nov 07, 2023)
15-59138191-C-T			Likely benign (Apr 17, 2021)
15-59138194-T-C			Uncertain significance (Jun 01, 2021)
15-59138212-T-C			Likely benign (Jun 30, 2023)
15-59138213-C-A			Uncertain significance (Aug 05, 2022)
15-59138224-T-C			Uncertain significance (Sep 06, 2022)
15-59138240-G-C			Uncertain significance (Dec 02, 2023)
15-59138259-G-A			Likely benign (Feb 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYO1E	protein_coding	protein_coding	ENST00000288235	28	237987

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000677	1.00	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.169	600	612	0.981	0.0000364	7363
Missense in Polyphen		261	298.5	0.87436		3582
Synonymous	-1.61	265	234	1.13	0.0000152	1995
Loss of Function	5.32	21	68.5	0.307	0.00000386	772

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000416	0.000416
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Myosins are actin-based motor molecules with ATPase activity. Unconventional myosins serve in intracellular movements. Their highly divergent tails bind to membranous compartments, which are then moved relative to actin filaments. Binds to membranes containing anionic phospholipids via its tail domain. Required for normal morphology of the glomerular basement membrane, normal development of foot processes by kidney podocytes and normal kidney function. In dendritic cells, may control the movement of class II-containing cytoplasmic vesicles along the actin cytoskeleton by connecting them with the actin network via ARL14EP and ARL14. {ECO:0000269|PubMed:11940582, ECO:0000269|PubMed:17257598, ECO:0000269|PubMed:20860408}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Primary Focal Segmental Glomerulosclerosis FSGS (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.0965
• rvis_EVS: -1.14
• rvis_percentile_EVS: 6.38

Haploinsufficiency Scores

• pHI: 0.390
• hipred: Y
• hipred_score: 0.706
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.846

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Myo1e
• 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); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); renal/urinary system phenotype; homeostasis/metabolism phenotype; muscle phenotype

Gene ontology

• Biological process: vasculogenesis;in utero embryonic development;glomerular filtration;nitrogen compound metabolic process;endocytosis;actin filament-based movement;glomerular basement membrane development;post-embryonic hemopoiesis;platelet-derived growth factor receptor signaling pathway;glomerular visceral epithelial cell development
• Cellular component: cytoplasm;cytoskeleton;brush border;cell-cell junction;adherens junction;actin cytoskeleton;myosin complex;clathrin-coated endocytic vesicle;extracellular exosome
• Molecular function: microfilament motor activity;motor activity;protein binding;calmodulin binding;ATP binding;phosphatidylinositol binding;ATPase activity, coupled;actin filament binding