MYOM3

Summary

MYOM3 (myomesin 3, HGNC:26679) is a protein-coding gene on chromosome 1p36.11, encoding Myomesin-3 (Q5VTT5). May link the intermediate filament cytoskeleton to the M-disk of the myofibrils in striated muscle.

Predicted to enable protein homodimerization activity. Predicted to be involved in sarcomere organization. Predicted to be located in cytoplasm. Predicted to be active in M band.

Source: NCBI Gene 127294 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 306 total
• MANE Select transcript: NM_152372

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26679
Approved symbol	MYOM3
Name	myomesin 3
Location	1p36.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ35961
Ensembl gene	ENSG00000142661
Ensembl biotype	protein_coding
OMIM	616832
Entrez	127294

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000338909, ENST00000374434, ENST00000448831, ENST00000475306, ENST00000958996, ENST00000958997, ENST00000958998, ENST00000958999, ENST00000959000

RefSeq mRNA: 1 — MANE Select: NM_152372 NM_152372

CCDS: CCDS41281

Canonical transcript exons

ENST00000374434 — 37 exons

Exon	Start	End
ENSE00001036491	24076159	24076273
ENSE00001036528	24081330	24081456
ENSE00001036557	24080016	24080194
ENSE00001036603	24068223	24068367
ENSE00001036624	24075319	24075475
ENSE00001130197	24067970	24068029
ENSE00001209336	24074160	24074269
ENSE00001209369	24084468	24084639
ENSE00001269847	24071969	24072013
ENSE00001269884	24082593	24082714
ENSE00001298529	24067021	24067088
ENSE00001305943	24071117	24071253
ENSE00001308604	24061946	24062109
ENSE00001311444	24064072	24064159
ENSE00001313938	24058924	24058979
ENSE00001322463	24063492	24063530
ENSE00001325915	24063126	24063234
ENSE00001391725	24082001	24082188
ENSE00001406157	24112031	24112135
ENSE00001463517	24061060	24061082
ENSE00001463521	24061273	24061309
ENSE00001463523	24065891	24066001
ENSE00001710631	24107993	24108073
ENSE00001884685	24056041	24057627
ENSE00002319606	24108476	24108654
ENSE00003491044	24092947	24093108
ENSE00003505955	24086644	24086827
ENSE00003510052	24107073	24107232
ENSE00003512664	24097923	24098011
ENSE00003518590	24089538	24089665
ENSE00003518846	24092174	24092315
ENSE00003535050	24095442	24095486
ENSE00003591711	24090065	24090118
ENSE00003605246	24094853	24094990
ENSE00003622252	24105920	24106077
ENSE00003630087	24090797	24090996
ENSE00003641470	24099680	24099775

Expression profiles

Bgee: expression breadth ubiquitous, 175 present calls, max score 98.49.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 2.1111 / max 336.9549, expressed in 111 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11033	1.8654	78
11034	0.1269	30
11032	0.0661	27
201409	0.0416	23
11031	0.0110	7

Top tissues by expression

249 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	98.49	gold quality
hindlimb stylopod muscle	UBERON:0004252	98.29	gold quality
gastrocnemius	UBERON:0001388	97.56	gold quality
heart left ventricle	UBERON:0002084	97.43	gold quality
left ventricle myocardium	UBERON:0006566	97.30	gold quality
cardiac ventricle	UBERON:0002082	97.20	gold quality
right atrium auricular region	UBERON:0006631	97.16	gold quality
cardiac muscle of right atrium	UBERON:0003379	97.12	gold quality
cardiac atrium	UBERON:0002081	96.91	gold quality
tibialis anterior	UBERON:0001385	96.65	gold quality
muscle of leg	UBERON:0001383	96.13	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	95.61	gold quality
skeletal muscle tissue	UBERON:0001134	94.12	gold quality
heart right ventricle	UBERON:0002080	93.47	gold quality
vastus lateralis	UBERON:0001379	92.32	gold quality
quadriceps femoris	UBERON:0001377	92.19	gold quality
heart	UBERON:0000948	91.82	gold quality
myocardium	UBERON:0002349	91.77	gold quality
deltoid	UBERON:0001476	91.43	silver quality
biceps brachii	UBERON:0001507	90.89	gold quality
muscle tissue	UBERON:0002385	90.57	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	89.76	gold quality
body of tongue	UBERON:0011876	87.27	gold quality
pancreatic ductal cell	CL:0002079	86.01	silver quality
adult mammalian kidney	UBERON:0000082	83.85	gold quality
buccal mucosa cell	CL:0002336	82.57	gold quality
kidney epithelium	UBERON:0004819	81.40	silver quality
kidney	UBERON:0002113	80.19	gold quality
tongue	UBERON:0001723	79.51	gold quality
upper arm skin	UBERON:0004263	77.78	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

44 targeting MYOM3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4713-3P	100.00	65.92	505
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-6753-3P	99.93	66.57	637
HSA-MIR-7107-3P	99.93	66.73	627
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-671-5P	99.52	67.11	1277
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4735-5P	99.43	68.49	1780
HSA-MIR-532-3P	99.34	65.76	1195
HSA-MIR-4254	99.11	65.15	1315
HSA-MIR-328-5P	99.08	64.65	1000
HSA-MIR-6885-5P	98.71	64.33	902
HSA-MIR-4725-5P	98.67	65.42	628

Literature-anchored findings (GeneRIF, showing 3)

• MYOM3 fragments hold promise for minimally invasive assessment of experimental therapies for DMD and other neuromuscular disorders. (PMID:26060189)
• mutations in Pakistani patients with dilated cardiomyopathy rs375563861 (C2orf40), rs143187236 (MYOM3), and rs564181443 (RTKN2) have 3 fold or higher allele frequency in South Asians than in the global populations (PMID:29886034)
• An acute eccentric exercise increases circulating myomesin 3 fragments. (PMID:33468054)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Myom3	ENSMUSG00000037139
rattus_norvegicus	Myom3	ENSRNOG00000032994
drosophila_melanogaster	mtgo	FBGN0259735
caenorhabditis_elegans		WBGENE00007944

Paralogs (11): MYOM2 (ENSG00000036448), FNDC3B (ENSG00000075420), MYBPC2 (ENSG00000086967), MYOM1 (ENSG00000101605), FNDC3A (ENSG00000102531), OBSL1 (ENSG00000124006), MYBPH (ENSG00000133055), MYBPC3 (ENSG00000134571), IGSF22 (ENSG00000179057), MYBPC1 (ENSG00000196091), MYBPHL (ENSG00000221986)

Protein

Protein identifiers

Myomesin-3 — Q5VTT5 (reviewed: Q5VTT5)

Alternative names: Myomesin family member 3

All UniProt accessions (1): Q5VTT5

UniProt curated annotations — full annotation on UniProt →

Function. May link the intermediate filament cytoskeleton to the M-disk of the myofibrils in striated muscle.

Subunit / interactions. Homodimer.

Subcellular location. Cytoplasm. Myofibril. Sarcomere. M line.

Isoforms (3)

UniProt ID	Names	Canonical?
Q5VTT5-1	1	yes
Q5VTT5-2	2
Q5VTT5-3	3

RefSeq proteins (1): NP_689585* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR003961	FN3_dom	Domain
IPR007110	Ig-like_dom	Domain
IPR013098	Ig_I-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036116	FN3_sf	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR050964	Striated_Muscle_Regulatory	Family

Pfam: PF00041, PF07679

UniProt features (34 total): sequence variant 12, domain 9, sequence conflict 5, splice variant 4, chain 1, region of interest 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VTT5-F1	76.55	0.19

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 69 (showing top): GCANCTGNY_MYOD_Q6, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION, TGACCTY_ERR1_Q2, GOBP_SARCOMERE_ORGANIZATION, GOBP_CELLULAR_COMPONENT_ASSEMBLY_INVOLVED_IN_MORPHOGENESIS, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, GOBP_ACTOMYOSIN_STRUCTURE_ORGANIZATION, GRE_C, GOBP_ORGANELLE_ASSEMBLY, GOMF_STRUCTURAL_CONSTITUENT_OF_MUSCLE, E12_Q6, GOBP_MUSCLE_CELL_DEVELOPMENT, TGACCTTG_SF1_Q6, GOBP_MUSCLE_CELL_DIFFERENTIATION, GOCC_M_BAND

GO Biological Process (1): sarcomere organization (GO:0045214)

GO Molecular Function (3): protein homodimerization activity (GO:0042803), protein binding (GO:0005515), identical protein binding (GO:0042802)

GO Cellular Component (2): M band (GO:0031430), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
myofibril assembly	1
actomyosin structure organization	1
identical protein binding	1
protein dimerization activity	1
binding	1
protein binding	1
A band	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

742 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MYOM3	SGCA	Q16586	552
MYOM3	MYOZ2	Q9NPC6	538
MYOM3	TNNI1	P19237	515
MYOM3	COX6A2	Q02221	472
MYOM3	MYOM2	P54296	434
MYOM3	MYL1	P05976	431
MYOM3	LRRC39	Q96DD0	427
MYOM3	ANKRD2	Q9GZV1	425
MYOM3	CSRP3	P50461	425
MYOM3	TNNT3	P45378	421
MYOM3	MYH7	P12883	418
MYOM3	TNNI2	P48788	413
MYOM3	MYL3	P08590	410
MYOM3	TNNT1	P13805	393
MYOM3	CKMT2	P17540	389

IntAct

6 interactions, top by confidence:

A	B	Type	Score
P		psi-mi:“MI:0914”(association)	0.350
MRPS23	MYH7B	psi-mi:“MI:0914”(association)	0.350
CSNK2B	TUBAL3	psi-mi:“MI:0914”(association)	0.350
AMOT	MYOM3	psi-mi:“MI:0915”(physical association)	0.000
MYOM3	ASH2L	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (10): MYOM3 (Affinity Capture-MS), MYOM3 (Affinity Capture-MS), MYOM3 (Two-hybrid), MYOM3 (Two-hybrid), MYOM3 (Two-hybrid), MYOM3 (Two-hybrid), MYOM3 (Two-hybrid), MYOM3 (Two-hybrid), MYOM3 (Affinity Capture-RNA), SPG21 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A087WV53, A1CS92, A2ABU4, A2Q908, A2RUH7, A4QZL9, D3ZHA0, O01761, O70468, O75369, O88599, P05548, P11275, P11730, P11798, P13466, P21333, P56276, P56741, P70402, P79280, Q05623, Q13177, Q13203, Q13557, Q14315, Q2GM53, Q2HJF7, Q2URB7, Q5FW53, Q5PQM4, Q5RCC4, Q5VTT5, Q5ZJJ9, Q5ZKI0, Q62422, Q63518, Q6C1H8, Q6P686, Q6PHZ2

Diamond homologs: A0JN74, A1L4K1, A2ABU4, A2ASS6, B1H278, H0UZ81, O00478, P18892, P82456, Q02084, Q13410, Q1XHU0, Q495X7, Q5BN31, Q5D7I0, Q5R7W8, Q5R996, Q5VTT5, Q6MFZ5, Q6UX41, Q6UXE8, Q70KF4, Q7YRV4, Q8BVW3, Q8BZ52, Q8N3K9, Q8VI40, Q8WVV5, Q8WZ42, Q91431, Q96F44, Q96KV6, Q96PL5, Q99PQ2, Q9ESN2, Q9HCM9, Q9JLN5, A2AAJ9, O88599, P12960

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

306 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	259
Likely benign	17
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4663 predictions. Top by Δscore:

Variant	Effect	Δscore
1:24057628:C:CC	acceptor_gain	1.0000
1:24057632:T:TC	acceptor_gain	1.0000
1:24058928:T:C	donor_gain	1.0000
1:24061058:A:AC	donor_gain	1.0000
1:24061059:C:CC	donor_gain	1.0000
1:24061940:GCTCA:G	donor_loss	1.0000
1:24061941:CTCAC:C	donor_loss	1.0000
1:24061942:TCA:T	donor_loss	1.0000
1:24061943:CACCT:C	donor_loss	1.0000
1:24061944:A:AG	donor_loss	1.0000
1:24061981:T:TA	donor_gain	1.0000
1:24061986:C:A	donor_gain	1.0000
1:24062105:TGTCT:T	acceptor_gain	1.0000
1:24062106:GTCT:G	acceptor_gain	1.0000
1:24062108:CT:C	acceptor_gain	1.0000
1:24062109:TC:T	acceptor_loss	1.0000
1:24062110:C:CC	acceptor_gain	1.0000
1:24062110:C:CG	acceptor_loss	1.0000
1:24062111:T:A	acceptor_loss	1.0000
1:24062114:A:AC	acceptor_gain	1.0000
1:24062114:A:C	acceptor_gain	1.0000
1:24062116:G:C	acceptor_gain	1.0000
1:24062116:G:GC	acceptor_gain	1.0000
1:24063122:TTAC:T	donor_loss	1.0000
1:24063123:TACTT:T	donor_loss	1.0000
1:24063124:A:AC	donor_gain	1.0000
1:24063124:A:T	donor_loss	1.0000
1:24063125:C:CA	donor_gain	1.0000
1:24063125:CT:C	donor_gain	1.0000
1:24063125:CTT:C	donor_gain	1.0000

AlphaMissense

9347 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:24057445:G:C	N1411K	0.999
1:24057445:G:T	N1411K	0.999
1:24076239:A:G	F874S	0.999
1:24080089:A:T	V838D	0.999
1:24080136:C:A	W822C	0.999
1:24080136:C:G	W822C	0.999
1:24080138:A:G	W822R	0.999
1:24080138:A:T	W822R	0.999
1:24081422:A:G	F772S	0.999
1:24082123:A:G	W720R	0.999
1:24082123:A:T	W720R	0.999
1:24082673:A:G	F671S	0.999
1:24086724:A:G	F573S	0.999
1:24097986:A:C	Y228D	0.999
1:24057446:T:A	N1411I	0.998
1:24057452:A:T	V1409D	0.998
1:24062047:A:G	L1278P	0.998
1:24064135:A:C	Y1187D	0.998
1:24074223:A:C	Y969D	0.998
1:24075383:A:G	W932R	0.998
1:24075383:A:T	W932R	0.998
1:24076220:A:C	N880K	0.998
1:24076220:A:T	N880K	0.998
1:24080096:A:C	Y836D	0.998
1:24080137:C:G	W822S	0.998
1:24080143:A:G	L820P	0.998
1:24082121:C:A	W720C	0.998
1:24082121:C:G	W720C	0.998
1:24082122:C:G	W720S	0.998
1:24082667:A:T	V673D	0.998

dbSNP variants (sampled 300 via entrez): RS1000022567 (1:24113097 G>A), RS1000031554 (1:24100729 A>G), RS1000120884 (1:24103222 C>T), RS1000215079 (1:24100909 A>G), RS1000272353 (1:24110523 C>T), RS1000306072 (1:24074343 G>A,T), RS1000329295 (1:24089849 T>C), RS1000425134 (1:24089856 A>G,T), RS1000485345 (1:24068745 G>A), RS1000498740 (1:24102191 C>T), RS1000514799 (1:24086568 G>C), RS1000606847 (1:24068545 T>C), RS1000612066 (1:24096399 C>T), RS1000612690 (1:24058175 G>A), RS1000775880 (1:24100543 C>G)

Disease associations

OMIM: gene MIM:616832 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001715_10	Bipolar disorder with mood-incongruent psychosis	4.000000e-06
GCST006098_9	Vigorous physical activity	5.000000e-09
GCST007576_232	Chronotype	3.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0008002	physical activity measurement
EFO:0008328	chronotype measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation	2
aristolochic acid I	increases expression	1
propionaldehyde	increases expression	1
bisphenol A	decreases methylation	1
tris(2-butoxyethyl) phosphate	affects expression	1
butyraldehyde	decreases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
incobotulinumtoxinA	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	decreases expression	1
Sunitinib	decreases expression	1
Leflunomide	decreases expression	1
Arsenic	decreases expression	1
Copper	decreases expression, affects cotreatment	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, increases expression	1
Folic Acid	decreases expression	1
Niclosamide	increases expression	1
Rotenone	decreases expression	1
Silicon Dioxide	increases expression	1
Urethane	decreases expression	1
Valproic Acid	increases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.