PACSIN3

Summary

PACSIN3 (protein kinase C and casein kinase substrate in neurons 3, HGNC:8572) is a protein-coding gene on chromosome 11p11.2, encoding Protein kinase C and casein kinase substrate in neurons protein 3 (Q9UKS6). Plays a role in endocytosis and regulates internalization of plasma membrane proteins.

This gene is a member of the protein kinase C and casein kinase substrate in neurons family. The encoded protein is involved in linking the actin cytoskeleton with vesicle formation. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 29763 — RefSeq curated summary.

At a glance

• Gene–disease (curated): myopathy (Moderate, GenCC)
• GWAS associations: 3
• Clinical variants (ClinVar): 96 total — 3 pathogenic
• Phenotypes (HPO): 23
• MANE Select transcript: NM_016223

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8572
Approved symbol	PACSIN3
Name	protein kinase C and casein kinase substrate in neurons 3
Location	11p11.2
Locus type	gene with protein product
Status	Approved
Aliases	SDPIII
Ensembl gene	ENSG00000165912
Ensembl biotype	protein_coding
OMIM	606513
Entrez	29763

Gene structure

Transcript identifiers

Ensembl transcripts: 64 — 63 protein_coding, 1 nonsense_mediated_decay

ENST00000298838, ENST00000524509, ENST00000525725, ENST00000528201, ENST00000528462, ENST00000530405, ENST00000530513, ENST00000531226, ENST00000532457, ENST00000533686, ENST00000539589, ENST00000889879, ENST00000889880, ENST00000889881, ENST00000889882, ENST00000889883, ENST00000889884, ENST00000889885, ENST00000889886, ENST00000889887, ENST00000889888, ENST00000889889, ENST00000889890, ENST00000889891, ENST00000889892, ENST00000889893, ENST00000889894, ENST00000889895, ENST00000889896, ENST00000889897, ENST00000889898, ENST00000889899, ENST00000889900, ENST00000889901, ENST00000889902, ENST00000889903, ENST00000889904, ENST00000889905, ENST00000889906, ENST00000889907, ENST00000889908, ENST00000889909, ENST00000938300, ENST00000938301, ENST00000938302, ENST00000938303, ENST00000938304, ENST00000950753, ENST00000950754, ENST00000950755, ENST00000950756, ENST00000950757, ENST00000950758, ENST00000950759, ENST00000950760, ENST00000950761, ENST00000950762, ENST00000950763, ENST00000950764, ENST00000950765, ENST00000950766, ENST00000950767, ENST00000950768, ENST00000950769

RefSeq mRNA: 3 — MANE Select: NM_016223 NM_001184974, NM_001184975, NM_016223

CCDS: CCDS31481

Canonical transcript exons

ENST00000298838 — 11 exons

Exon	Start	End
ENSE00001097988	47183004	47183069
ENSE00001219179	47186349	47186434
ENSE00001219252	47182674	47182764
ENSE00001636253	47177522	47178046
ENSE00001675362	47179159	47179279
ENSE00001685188	47178894	47179030
ENSE00003461083	47178366	47178487
ENSE00003545455	47182403	47182559
ENSE00003590865	47180455	47180690
ENSE00003608057	47180186	47180341
ENSE00003618002	47179411	47179586

Expression profiles

Bgee: expression breadth ubiquitous, 216 present calls, max score 98.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.8276 / max 160.7159, expressed in 1428 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
119557	5.8935	1417
119554	0.3065	119
119551	0.2709	36
119552	0.1215	27
119556	0.0931	39
119553	0.0790	25
119555	0.0418	16
119550	0.0213	16

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	98.82	gold quality
hindlimb stylopod muscle	UBERON:0004252	98.66	gold quality
gastrocnemius	UBERON:0001388	98.45	gold quality
muscle of leg	UBERON:0001383	97.63	gold quality
body of tongue	UBERON:0011876	96.68	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	96.64	gold quality
heart left ventricle	UBERON:0002084	96.25	gold quality
muscle organ	UBERON:0001630	96.13	gold quality
skeletal muscle organ	UBERON:0014892	96.13	gold quality
right atrium auricular region	UBERON:0006631	96.07	gold quality
cardiac ventricle	UBERON:0002082	95.82	gold quality
right adrenal gland cortex	UBERON:0035827	95.35	gold quality
right adrenal gland	UBERON:0001233	95.17	gold quality
left adrenal gland	UBERON:0001234	94.92	gold quality
left adrenal gland cortex	UBERON:0035825	94.85	gold quality
cardiac atrium	UBERON:0002081	94.52	gold quality
adrenal cortex	UBERON:0001235	94.31	gold quality
sural nerve	UBERON:0015488	94.26	gold quality
gluteal muscle	UBERON:0002000	93.94	gold quality
triceps brachii	UBERON:0001509	93.75	gold quality
lower esophagus mucosa	UBERON:0035834	93.63	gold quality
heart	UBERON:0000948	93.62	gold quality
skeletal muscle tissue	UBERON:0001134	93.56	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	92.98	gold quality
adrenal gland	UBERON:0002369	92.74	gold quality
esophagus mucosa	UBERON:0002469	92.57	gold quality
tongue	UBERON:0001723	92.50	gold quality
muscle layer of sigmoid colon	UBERON:0035805	92.38	gold quality
minor salivary gland	UBERON:0001830	92.07	gold quality
pharyngeal mucosa	UBERON:0000355	92.04	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.41

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting PACSIN3, 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-6867-5P	100.00	82.21	3464
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-449B-3P	99.20	67.24	1047
HSA-MIR-4292	99.16	65.57	1767
HSA-MIR-6791-5P	99.16	65.92	1844
HSA-MIR-873-5P	98.84	66.90	1348
HSA-MIR-147A	98.33	66.40	795
HSA-MIR-6773-3P	98.17	65.51	1213
HSA-MIR-3127-5P	97.52	65.24	786
HSA-MIR-592	96.59	67.59	817

Literature-anchored findings (GeneRIF, showing 4)

• PACSIN3 has a novel function as an up-regulator in the signaling of proHB-EGF shedding induced by TPA and angiotensin II (PMID:12952982)
• PACSIN 3 acts as an auxiliary protein of TRPV4 channel that not only affects the channel’s subcellular localization but also modulates its function in a stimulus-specific manner. (PMID:18174177)
• Rigidity of wedge loop in PACSIN 3 protein is a key factor in dictating diameters of tubules (PMID:22573331)
• Show that in neuroendocrine chromaffin cells fusion pore expansion and catecholamine release are limited specifically by mutation of syndapin 3. (PMID:24500282)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	pacsin3	ENSDARG00000099339
mus_musculus	Pacsin3	ENSMUSG00000027257
rattus_norvegicus	Pacsin3	ENSRNOG00000014204
drosophila_melanogaster	Synd	FBGN0053094
caenorhabditis_elegans		WBGENE00018467

Paralogs (2): PACSIN2 (ENSG00000100266), PACSIN1 (ENSG00000124507)

Protein

Protein identifiers

Protein kinase C and casein kinase substrate in neurons protein 3 — Q9UKS6 (reviewed: Q9UKS6)

Alternative names: SH3 domain-containing protein 6511

All UniProt accessions (9): A0A0C4DGG1, E9PIY1, E9PIZ6, E9PJ33, E9PJ75, E9PNM9, E9PQ12, Q9UKS6, H0YDM6

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in endocytosis and regulates internalization of plasma membrane proteins. Overexpression impairs internalization of SLC2A1/GLUT1 and TRPV4 and increases the levels of SLC2A1/GLUT1 and TRPV4 at the cell membrane. Inhibits the TRPV4 calcium channel activity.

Subunit / interactions. Homodimer. May form heterooligomers with other PACSINs. Interacts (via SH3 domain) with DNM1, SYNJ1 and WASL. Interacts with TRPV4.

Subcellular location. Cytoplasm. Cell membrane.

Tissue specificity. Widely expressed, with highest levels in heart and skeletal muscle, intermediate levels in placenta, liver and pancreas, and very low levels in brain, lung and kidney.

Post-translational modifications. Phosphorylated by casein kinase 2 (CK2) and protein kinase C (PKC).

Disease relevance. Congenital myopathy 27 (CMYO27) [MIM:621343] A form of congenital myopathy, a clinically and genetically heterogeneous group of muscle disorders characterized by hypotonia and muscle weakness typically noticed at birth or during the neonatal period, and specific pathological features on muscle biopsy. CMYO27 is an autosomal recessive form with mild features beginning in early childhood. Affected children show delayed motor development, exercise intolerance, and easy fatigability. Serum creatine kinase is increased. Fiber size variation and atrophic fibers are seen on muscle biopsy. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The F-BAR domain forms a coiled coil and mediates membrane-binding and membrane tubulation.

Similarity. Belongs to the PACSIN family.

RefSeq proteins (3): NP_001171903, NP_001171904, NP_057307* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001060	FCH_dom	Domain
IPR001452	SH3_domain	Domain
IPR027267	AH/BAR_dom_sf	Homologous_superfamily
IPR031160	F_BAR_dom	Domain
IPR036028	SH3-like_dom_sf	Homologous_superfamily

Pfam: PF00611, PF14604

UniProt features (17 total): modified residue 7, domain 2, sequence variant 2, region of interest 2, compositionally biased region 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UKS6-F1	87.12	0.76

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (7): 319, 324, 327, 354, 383, 276, 303

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-8856828	Clathrin-mediated endocytosis

MSigDB gene sets: 151 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, YAATNRNNNYNATT_UNKNOWN, HNF3ALPHA_Q6, GCANCTGNY_MYOD_Q6, MAZ_Q6, ROVERSI_GLIOMA_COPY_NUMBER_UP, GOBP_PLASMA_MEMBRANE_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_ENDOCYTOSIS, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, LHX3_01, CAGCTG_AP4_Q5, SREBP1_02

GO Biological Process (7): endocytosis (GO:0006897), cytoskeleton organization (GO:0007010), regulation of endocytosis (GO:0030100), negative regulation of endocytosis (GO:0045806), positive regulation of membrane protein ectodomain proteolysis (GO:0051044), negative regulation of calcium ion transport (GO:0051926), plasma membrane tubulation (GO:0097320)

GO Molecular Function (6): phospholipid binding (GO:0005543), cytoskeletal protein binding (GO:0008092), lipid binding (GO:0008289), calcium channel inhibitor activity (GO:0019855), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (7): cytoplasm (GO:0005737), endosome (GO:0005768), cytosol (GO:0005829), plasma membrane (GO:0005886), extracellular exosome (GO:0070062), endomembrane system (GO:0012505), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Membrane Trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
endocytosis	2
protein binding	2
binding	2
vesicle budding from membrane	1
membrane invagination	1
vesicle-mediated transport	1
import into cell	1
organelle organization	1
regulation of cellular component organization	1
regulation of vesicle-mediated transport	1
regulation of endocytosis	1
negative regulation of transport	1
negative regulation of cellular component organization	1
membrane protein ectodomain proteolysis	1
positive regulation of protein catabolic process	1
positive regulation of proteolysis	1
regulation of membrane protein ectodomain proteolysis	1
calcium ion transport	1
negative regulation of monoatomic ion transport	1
regulation of calcium ion transport	1
plasma membrane organization	1
lipid binding	1
calcium channel regulator activity	1
calcium channel activity	1
ion channel inhibitor activity	1
intracellular anatomical structure	1
endomembrane system	1
cytoplasmic vesicle	1
cytoplasm	1
membrane	1
cell periphery	1
extracellular vesicle	1
vacuole	1
plasma membrane	1

Protein interactions and networks

STRING

1224 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PACSIN3	TRPV4	Q9HBA0	802
PACSIN3	WASL	O00401	704
PACSIN3	ADAM9	Q13443	681
PACSIN3	TRIP10	Q15642	674
PACSIN3	SYNJ1	O43426	574
PACSIN3	FES	P07332	556
PACSIN3	ADAM12	O43184	552
PACSIN3	FCHSD1	Q86WN1	529
PACSIN3	DNM2	P50570	514
PACSIN3	DNM1	Q05193	479
PACSIN3	MAP7	Q14244	473
PACSIN3	CAV1	Q03135	449
PACSIN3	GIT1	Q9Y2X7	445
PACSIN3	ADAM10	O14672	430
PACSIN3	FCHO2	Q0JRZ9	426

IntAct

140 interactions, top by confidence:

A	B	Type	Score
PACSIN1	PACSIN3	psi-mi:“MI:0915”(physical association)	0.900
PACSIN3	PACSIN1	psi-mi:“MI:0915”(physical association)	0.900
CCDC22	VPS26C	psi-mi:“MI:0914”(association)	0.790
PACSIN1	COBL	psi-mi:“MI:0914”(association)	0.750
PACSIN3	PACSIN2	psi-mi:“MI:0915”(physical association)	0.740
COMMD4	VPS26C	psi-mi:“MI:0914”(association)	0.730
PACSIN1	COBLL1	psi-mi:“MI:0914”(association)	0.660
ADAM15	PACSIN3	psi-mi:“MI:0915”(physical association)	0.650
PACSIN3	ADAM15	psi-mi:“MI:0915”(physical association)	0.650
CCDC93	VPS26C	psi-mi:“MI:0914”(association)	0.640
PACSIN3	FASLG	psi-mi:“MI:0915”(physical association)	0.590
FASLG	PACSIN3	psi-mi:“MI:0915”(physical association)	0.590
SPRY2	PACSIN3	psi-mi:“MI:0915”(physical association)	0.560
PACSIN3	LGALS13	psi-mi:“MI:0915”(physical association)	0.560
LGALS13	PACSIN3	psi-mi:“MI:0915”(physical association)	0.560
KRTAP12-2	PACSIN3	psi-mi:“MI:0915”(physical association)	0.560
WASL	PACSIN3	psi-mi:“MI:0915”(physical association)	0.560
SMARCD1	PACSIN3	psi-mi:“MI:0915”(physical association)	0.560
TNPO2	PACSIN3	psi-mi:“MI:0915”(physical association)	0.560
	PACSIN3	psi-mi:“MI:0915”(physical association)	0.560
PACSIN3	PACSIN3	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (208): PACSIN3 (Two-hybrid), PACSIN3 (Two-hybrid), PACSIN3 (Two-hybrid), PACSIN1 (Two-hybrid), PACSIN3 (Affinity Capture-MS), COBL (Affinity Capture-MS), PACSIN2 (Affinity Capture-MS), COBLL1 (Affinity Capture-MS), PACSIN3 (Co-fractionation), PACSIN3 (Co-fractionation), PACSIN3 (Co-fractionation), PACSIN3 (Co-fractionation), PACSIN3 (Co-fractionation), PACSIN3 (Co-fractionation), PACSIN3 (Co-fractionation)

ESM2 similar proteins: A7MBI0, D3ZYR1, O13154, O43586, O55148, O60749, O60861, P09760, P16591, P70451, P97531, P97814, Q0JRZ9, Q15642, Q2HWF0, Q3KR97, Q3UQN2, Q4V920, Q5R411, Q5R807, Q5RCJ1, Q5T0N5, Q5U3Q6, Q60780, Q61644, Q6DCZ7, Q6GNV5, Q6GUF4, Q8CJ53, Q8I190, Q8I1A6, Q8I1C0, Q8I1I3, Q8K012, Q8T390, Q91VH2, Q99JB8, Q99M15, Q99N27, Q9BY11

Diamond homologs: A0A0G2JV04, A0JNB0, A1A5H8, A1CEK6, A1DFN5, A1Y2K1, A2QW93, A3LXQ8, A4RF61, A5D8S5, A6H7G2, A6QLK6, A7MBI0, D3ZG83, F1RDG9, O13154, O42287, O43125, O55043, O74749, O75791, O89100, P00523, P00525, P00526, P00528, P05480, P06241, P09324, P10936, P12931, P13115, P13116, P13406, P14084, P14085, P15054, P25020, P27446, P27447

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 126 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Parasite infection	5	22.5×	4e-04
Leishmania phagocytosis	5	22.5×	4e-04
Signaling by high-kinase activity BRAF mutants	5	20.6×	4e-04
Sensory processing of sound	5	20.0×	4e-04
MAP2K and MAPK activation	5	18.5×	4e-04
Fcgamma receptor (FCGR) dependent phagocytosis	5	18.1×	4e-04
FCGR3A-mediated phagocytosis	7	17.0×	1e-04
Signaling by moderate kinase activity BRAF mutants	5	16.5×	5e-04

GO biological processes:

GO term	Partners	Fold	FDR
platelet aggregation	6	21.1×	4e-04
epidermal growth factor receptor signaling pathway	6	15.5×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	0
Uncertain significance	85
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
4087699	NM_016223.5(PACSIN3):c.609_610del (p.Lys203fs)	Pathogenic
4087700	NM_016223.5(PACSIN3):c.592G>T (p.Glu198Ter)	Pathogenic
4087701	NM_016223.5(PACSIN3):c.270_277del (p.Leu91fs)	Pathogenic

SpliceAI

2054 predictions. Top by Δscore:

Variant	Effect	Δscore
11:47178044:CCC:C	acceptor_gain	1.0000
11:47178045:CC:C	acceptor_gain	1.0000
11:47178045:CCC:C	acceptor_gain	1.0000
11:47178046:CC:C	acceptor_gain	1.0000
11:47178047:C:CC	acceptor_gain	1.0000
11:47178361:GGTAC:G	donor_loss	1.0000
11:47178362:GTACC:G	donor_loss	1.0000
11:47178363:TA:T	donor_loss	1.0000
11:47178365:CCTGC:C	donor_loss	1.0000
11:47178368:G:A	donor_gain	1.0000
11:47178381:G:C	donor_gain	1.0000
11:47178392:T:TA	donor_gain	1.0000
11:47178483:CCGTG:C	acceptor_gain	1.0000
11:47178484:CGTG:C	acceptor_gain	1.0000
11:47178484:CGTGC:C	acceptor_gain	1.0000
11:47178485:GTG:G	acceptor_gain	1.0000
11:47178486:TG:T	acceptor_gain	1.0000
11:47178486:TGCTG:T	acceptor_loss	1.0000
11:47178487:GC:G	acceptor_loss	1.0000
11:47178488:C:CC	acceptor_gain	1.0000
11:47178881:T:A	donor_gain	1.0000
11:47178892:AC:A	donor_gain	1.0000
11:47178893:CC:C	donor_gain	1.0000
11:47179164:A:AC	donor_gain	1.0000
11:47179165:C:CC	donor_gain	1.0000
11:47179278:ACCT:A	acceptor_loss	1.0000
11:47179279:CCTA:C	acceptor_loss	1.0000
11:47179406:CATA:C	donor_loss	1.0000
11:47179407:ATACT:A	donor_loss	1.0000
11:47179409:A:AC	donor_gain	1.0000

AlphaMissense

2783 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:47177962:G:T	P415H	1.000
11:47177963:G:A	P415S	1.000
11:47177966:A:C	Y414D	1.000
11:47178003:C:A	W401C	1.000
11:47178003:C:G	W401C	1.000
11:47178005:A:G	W401R	1.000
11:47178005:A:T	W401R	1.000
11:47178374:A:G	F384S	1.000
11:47177963:G:T	P415T	0.999
11:47177966:A:T	Y414N	0.999
11:47177971:C:A	G412V	0.999
11:47177971:C:T	G412D	0.999
11:47177996:C:G	G404R	0.999
11:47178004:C:G	W401S	0.999
11:47178380:A:G	L382P	0.999
11:47178383:T:A	E381V	0.999
11:47178411:A:C	Y372D	0.999
11:47180495:A:G	F136S	0.999
11:47177965:T:G	Y414S	0.998
11:47177966:A:G	Y414H	0.998
11:47177972:C:G	G412R	0.998
11:47177995:C:T	G404D	0.998
11:47177996:C:A	G404C	0.998
11:47178008:C:G	G400R	0.998
11:47178017:C:G	D397H	0.998
11:47178037:A:G	L390P	0.998
11:47178374:A:C	F384C	0.998
11:47178380:A:T	L382Q	0.998
11:47178383:T:C	E381G	0.998
11:47178384:C:T	E381K	0.998

dbSNP variants (sampled 300 via entrez): RS1000520132 (11:47187385 G>A,C,T), RS1000727989 (11:47177127 C>A,T), RS1000796273 (11:47183088 G>A), RS1000843883 (11:47181044 C>T), RS1000863849 (11:47184354 C>T), RS1000913019 (11:47182796 T>C), RS1001294397 (11:47180903 C>T), RS1001516488 (11:47183446 G>A,C), RS1001632854 (11:47178313 C>T), RS1001635330 (11:47177222 A>C), RS1001693304 (11:47177855 T>C), RS1001900860 (11:47182043 T>A), RS1001966942 (11:47183157 G>T), RS1002288544 (11:47187613 G>A), RS1002373845 (11:47182033 T>C)

Disease associations

OMIM: gene MIM:606513 | disease phenotypes: MIM:621343

GenCC curated gene-disease

Disease	Classification	Inheritance
myopathy	Moderate	Autosomal recessive

Mondo (2): congenital myopathy 27 (MONDO:0979897), myopathy (MONDO:0005336)

Orphanet (0):

HPO phenotypes

23 total (23 of 23 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0001252	Hypotonia
HP:0001270	Motor delay
HP:0001324	Muscle weakness
HP:0001508	Failure to thrive
HP:0003236	Elevated circulating creatine kinase concentration
HP:0003326	Myalgia
HP:0003388	Easy fatigability
HP:0003546	Exercise intolerance
HP:0003557	Increased variability in muscle fiber diameter
HP:0003593	Infantile onset
HP:0003687	Centrally nucleated skeletal muscle fibers
HP:0003719	Muscle mounding
HP:0003760	Percussion-induced rapid rolling muscle contractions
HP:0011463	Childhood onset
HP:0011968	Feeding difficulties
HP:0012450	Chronic constipation
HP:0031956	Elevated circulating aspartate aminotransferase concentration
HP:0031964	Elevated circulating alanine aminotransferase concentration
HP:0032232	Elevated circulating CK-MB concentration
HP:0033834	Malaise
HP:0040129	Abnormal nerve conduction velocity
HP:0100297	Increased endomysial connective tissue

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST003338_4	Waist-to-hip ratio adjusted for body mass index	8.000000e-07
GCST004521_165	Autism spectrum disorder or schizophrenia	3.000000e-08
GCST007825_4	Alzheimer’s disease or fasting glucose levels (pleiotropy)	3.000000e-16

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

43 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, increases expression, decreases expression	3
entinostat	increases expression, affects cotreatment	2
Benzo(a)pyrene	affects methylation, increases expression	2
Tobacco Smoke Pollution	affects expression	2
Cyclosporine	decreases expression, increases expression	2
FR900359	affects phosphorylation	1
methylmercuric chloride	decreases expression	1
titanium dioxide	decreases expression	1
ochratoxin A	decreases expression	1
coumarin	decreases phosphorylation	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
abrine	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
dorsomorphin	increases expression, affects cotreatment	1
bisphenol S	affects expression	1
jinfukang	increases expression	1
NSC 689534	affects binding, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Allergens	increases expression	1
Arsenic	increases abundance, increases expression	1
Caffeine	affects phosphorylation	1
Copper	affects binding, decreases expression	1
Doxorubicin	increases expression	1
Ivermectin	decreases expression	1
Lipopolysaccharides	affects cotreatment, decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B3D7	Abcam HEK293T PACSIN3 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00120055	PHASE4	COMPLETED	Association Between Systemic Exposure of Atorvastatin and Metabolites and Atorvastatin-induced Myotoxicity
NCT03633565	PHASE4	UNKNOWN	Comparative Study of Strategies for Management of Duchenne Myopathy (DM)
NCT01225614	PHASE3	UNKNOWN	Efficacy and Tolerance of Early Launching of Nocturnal Non Invasive
NCT00278564	PHASE1	TERMINATED	Stem Cell Transplantation in Idiopathic Inflammatory Myopathy Diseases
NCT01642056	PHASE1/PHASE2	COMPLETED	EPI-743 for Metabolism or Mitochondrial Disorders
NCT02124070	PHASE1/PHASE2	WITHDRAWN	Therapeutic Effect of Recombinant Human Growth Hormone (rhGH) on the Myopathy of Cystinosis
NCT00549029	Not specified	UNKNOWN	The Association of Genetic Polymorphisms With Statin-Induced Myopathy.
NCT00767130	Not specified	UNKNOWN	DNA Diagnostic System for Statin Safety and Efficacy
NCT00922428	Not specified	COMPLETED	PASCOE-Agil HOM-Injektopas in the Treatment of Rheumatic Disorders
NCT00937001	Not specified	ACTIVE_NOT_RECRUITING	Critical Illness Myopathy as a Cause of Debilitating ICU-Acquired Weakness
NCT00990834	Not specified	WITHDRAWN	Muscle Characteristics Associated With Statin Therapy
NCT01022450	Not specified	UNKNOWN	Study of the Causes of the Breakdown of Muscle Fibers in Hospitalized Patients
NCT01040650	Not specified	TERMINATED	Metabolic Features of Post-Myopathy Patients Associated With Statin Treatment
NCT01047163	Not specified	COMPLETED	Maintenance of Muscle Mass in Older People: the Negative Impact of Statin Therapy
NCT01270269	Not specified	COMPLETED	ACT-ICU Study: Activity and Cognitive Therapy in the Intensive Care Unit
NCT01353430	Not specified	RECRUITING	Characterization of Inclusion Body Myopathy Associated With Paget’s Disease of Bone and Frontotemporal Dementia (IBMPFD)
NCT01395563	Not specified	WITHDRAWN	Strength Training on Pancreatic Cancer
NCT01530841	Not specified	COMPLETED	Efficacy and Tolerance of AVAPS Mode in Myotonic Dystrophy
NCT01547767	Not specified	COMPLETED	Investigations Into ISCU Myopathy or Iron Sulfur Scaffold U Protein Myopathy
NCT01702987	Not specified	COMPLETED	Evaluation of Ubiquinol on Mitochondrial Oxidative Capacity in Statin Patients Using 31PMRS
NCT01790178	Not specified	COMPLETED	Ultrasound in Muscle Biopsy
NCT02011282	Not specified	COMPLETED	Electro-Neuro-Muscular Stimulation in ICU
NCT02104921	Not specified	COMPLETED	Innovative Ultrasound Technology in Neuromuscular Disease
NCT02118805	Not specified	COMPLETED	Innovative Measures of Speech and Swallowing Dysfunction in Neurological Disorders
NCT02235220	Not specified	UNKNOWN	Reduction of Masticatory Muscle Activity by Restoring Canine Guidance
NCT02247895	Not specified	TERMINATED	Treatment of Muscle Weakness in Critically Ill Patients
NCT02315339	Not specified	TERMINATED	European Home Mechanical Ventilation Registry
NCT02442986	Not specified	COMPLETED	Neurological Outcome in Surgical and Non-surgical Septic Patients
NCT02706314	Not specified	COMPLETED	Impact of Human Blood Serum From Critically Ill Patients on Human Colon Neuronal Networks.
NCT02765828	Not specified	COMPLETED	Identification of Tongue Involvement in Late-Onset Pompe Disease
NCT03042286	Not specified	UNKNOWN	SAPhIRE Statin Adverse Drug Reaction
NCT03141749	Not specified	COMPLETED	Venous Thromboembolism in DM1
NCT03660969	Not specified	ACTIVE_NOT_RECRUITING	Reliability of Cardiac Troponins for the Diagnosis of Myocardial Infarction in the Presence of Skeletal Muscle Disease
NCT03749538	Not specified	RECRUITING	Acute Transcranial Direct Current Stimulation in Patients With Systemic Autoimmune Myopathies
NCT03751644	Not specified	COMPLETED	Peripherical Neuromuscular Electrical Stimulation in Systemic Autoimmune Myopathies
NCT03998540	Not specified	UNKNOWN	Improvement of DIAgnostic and Phenotype-genotype Correlation Studies in Patients With MYOpathy Suspected of TITinopathy
NCT04678635	Not specified	RECRUITING	Chronic Transcranial Direct Current Stimulation in Patients With Systemic Autoimmune Myopathies
NCT04881214	Not specified	UNKNOWN	COVID-19 Pneumonia: Pulmonary Physiology, Health-related Quality of Life and Benefit of a Rehabilitation Program
NCT04941079	Not specified	UNKNOWN	Safety and Efficacy of Inactivated SARS-CoV-2 Vaccine in Immune-related Myopathy (Myasthenia Gravis and Inflammatory Myopathy) Patients ：a Prospective Observational Study
NCT05599568	Not specified	RECRUITING	Repeated Bout Effect i Neuromuscular Diseases