RMDN3

Summary

RMDN3 (regulator of microtubule dynamics 3, HGNC:25550) is a protein-coding gene on chromosome 15q15.1, encoding Regulator of microtubule dynamics protein 3 (Q96TC7). Involved in cellular calcium homeostasis regulation.

Enables microtubule binding activity. Involved in intracellular calcium ion homeostasis. Located in several cellular components, including intercellular bridge; mitochondrial outer membrane; and spindle.

Source: NCBI Gene 55177 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 79 total — 1 pathogenic
• MANE Select transcript: NM_018145

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25550
Approved symbol	RMDN3
Name	regulator of microtubule dynamics 3
Location	15q15.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10579, PTPIP51, RMD3
Ensembl gene	ENSG00000137824
Ensembl biotype	protein_coding
OMIM	611873
Entrez	55177

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 22 protein_coding, 3 retained_intron, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000260385, ENST00000338376, ENST00000557831, ENST00000558232, ENST00000558364, ENST00000558560, ENST00000558777, ENST00000560460, ENST00000560588, ENST00000560779, ENST00000560905, ENST00000862129, ENST00000862130, ENST00000862131, ENST00000862132, ENST00000862133, ENST00000862134, ENST00000862135, ENST00000862136, ENST00000862137, ENST00000862138, ENST00000918999, ENST00000919000, ENST00000919001, ENST00000951448, ENST00000951449, ENST00000951450, ENST00000951451

RefSeq mRNA: 6 — MANE Select: NM_018145 NM_001304802, NM_001323894, NM_001323895, NM_001323896, NM_001323897, NM_018145

CCDS: CCDS10063

Canonical transcript exons

ENST00000338376 — 13 exons

Exon	Start	End
ENSE00000883922	40754597	40754790
ENSE00001029653	40755083	40755254
ENSE00003482422	40737628	40737726
ENSE00003510412	40735887	40736594
ENSE00003513194	40751986	40752178
ENSE00003550115	40737288	40737341
ENSE00003575584	40744047	40744149
ENSE00003603792	40751426	40751569
ENSE00003633617	40740133	40740193
ENSE00003645635	40737965	40738042
ENSE00003662527	40738501	40738576
ENSE00003688648	40744977	40745259
ENSE00003694028	40737124	40737204

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 94.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.0709 / max 172.1284, expressed in 1819 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
149504	25.0549	1819
149502	0.0103	6
149503	0.0057	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	94.60	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	94.06	gold quality
cerebellar hemisphere	UBERON:0002245	93.97	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.95	gold quality
jejunal mucosa	UBERON:0000399	93.93	gold quality
cerebellar cortex	UBERON:0002129	93.92	gold quality
anterior cingulate cortex	UBERON:0009835	93.89	gold quality
cingulate cortex	UBERON:0003027	93.88	gold quality
prefrontal cortex	UBERON:0000451	93.61	gold quality
right frontal lobe	UBERON:0002810	93.54	gold quality
spinal cord	UBERON:0002240	93.49	gold quality
amygdala	UBERON:0001876	93.42	gold quality
duodenum	UBERON:0002114	93.34	gold quality
cerebellum	UBERON:0002037	93.26	gold quality
Brodmann (1909) area 9	UBERON:0013540	93.25	gold quality
olfactory bulb	UBERON:0002264	92.92	silver quality
upper lobe of left lung	UBERON:0008952	92.70	gold quality
right lobe of liver	UBERON:0001114	92.57	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	92.40	gold quality
upper lobe of lung	UBERON:0008948	92.37	gold quality
hypothalamus	UBERON:0001898	92.29	gold quality
putamen	UBERON:0001874	92.19	gold quality
frontal cortex	UBERON:0001870	92.13	gold quality
neocortex	UBERON:0001950	92.13	gold quality
right lung	UBERON:0002167	92.02	gold quality
sural nerve	UBERON:0015488	92.00	gold quality
caudate nucleus	UBERON:0001873	91.99	gold quality
nucleus accumbens	UBERON:0001882	91.94	gold quality
substantia nigra	UBERON:0002038	91.51	gold quality
small intestine	UBERON:0002108	91.45	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

39 targeting RMDN3, 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-499A-5P	99.98	70.79	1323
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-498-5P	99.76	69.64	1807
HSA-MIR-5002-5P	99.76	70.84	1763
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-3609	99.52	69.89	2587
HSA-MIR-548AH-5P	99.52	69.73	2626
HSA-MIR-4777-5P	99.33	67.53	1148
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-4796-3P	99.08	68.38	1681
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-224-5P	98.33	70.12	1256
HSA-MIR-6771-3P	98.20	66.53	971
HSA-MIR-12127	97.93	66.67	793

Literature-anchored findings (GeneRIF, showing 18)

• PTPIP51 might be involved in the regulation of cellular processes associated with differentiation, movement, or cytoskeletal organization (PMID:15609043)
• PTPIP51 is a mitochondrial protein with apoptosis-inducing function and that the N-terminal TM domain is required for both the correct targeting of the protein to mitochondria and its apoptotic functions. (PMID:16820967)
• PTPIP51 and PTP1B, play a role in differentiation and apoptosis of the cytotrophoblast and syncytiotrophoblast, respectively. Moreover, PTPIP51 may also serve as a cellular signaling partner in angiogenesis and vascular remodeling. (PMID:18854601)
• FAM82A2 is expressed in keratinocyte carcinoma and their surrounding stroma. (PMID:19012732)
• The results clearly point toward a strong association between PTPIP51 expression and differentiation in human muscle cells. (PMID:19124842)
• The promoter methylation status of PTPIP51 seems to influence the expression of PTPIP51, which was seen as elevated in the prostate carcinoma. (PMID:19691131)
• PTPIP51 expression was restricted to myeloid precursor cells undergoing differentiation. In blood cells therefore, PTPIP51 expression is restricted to differentiating and mature neutrophil granulocytes. (PMID:20627780)
• PTPIP51 is phosphorylated by Lyn and c-Src kinases lacking dephosphorylation by PTP1B in acute myeloid leukemia. (PMID:21513978)
• In glioblastoma PTPIP51 expression increases with the grade of malignancy and PTPIP51 interacts in situ with 14-3-3ss and PTP1B. (PMID:21972092)
• The presented data confirms a tyrosine phosphorylation-dependent interaction of PTPIP51 with 14-3-3beta and Raf-1 in vivo and a tyrosine-dependent interaction profile with DAGKalpha and PKA. (PMID:22544307)
• PTPIP51 is regulated by its phosphorylation status combined with a thereby induced subcellular redistribution. (PMID:24501773)
• High PTPIP51 expression is associated with glioblastoma. (PMID:25862004)
• the latest findings concerning PTPIP51 protein function, regulation and protein complex formation with regard to the involved signaling pathways and subcellular compartments (review) (PMID:27734150)
• Study shows that the VAPB-PTPIP51 tethers regulate autophagy and demonstrates that overexpression of VAPB or PTPIP51 to tighten endoplasmic reticulum-mitochondria contacts impairs, whereas small interfering RNA-mediated loss of VAPB or PTPIP51 to loosen contacts stimulates, autophagosome formation. (PMID:28132811)
• Disruption of endoplasmic reticulum-mitochondria tethering proteins in post-mortem Alzheimer’s disease brain. (PMID:32682953)
• Phospholipid transfer function of PTPIP51 at mitochondria-associated ER membranes. (PMID:33938112)
• PTPIP51 inhibits non-small-cell lung cancer by promoting PTEN-mediated EGFR degradation. (PMID:35240162)
• Stimulating VAPB-PTPIP51 ER-mitochondria tethering corrects FTD/ALS mutant TDP43 linked Ca[2+] and synaptic defects. (PMID:38395965)

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio	rmdn3	ENSDARG00000041407
mus_musculus	Rmdn3	ENSMUSG00000070730
rattus_norvegicus	Rmdn3	ENSRNOG00000011690
caenorhabditis_elegans		WBGENE00007190
caenorhabditis_elegans		WBGENE00007786
caenorhabditis_elegans		WBGENE00011501
caenorhabditis_elegans		WBGENE00012976
caenorhabditis_elegans		WBGENE00015855
caenorhabditis_elegans		WBGENE00020070

Paralogs (3): RMDN2 (ENSG00000115841), TEX10 (ENSG00000136891), RMDN1 (ENSG00000176623)

Protein

Protein identifiers

Regulator of microtubule dynamics protein 3 — Q96TC7 (reviewed: Q96TC7)

Alternative names: Cerebral protein 10, Protein FAM82A2, Protein FAM82C, Protein tyrosine phosphatase-interacting protein 51, TCPTP-interacting protein 51

All UniProt accessions (5): Q96TC7, H0YLG5, H0YLV7, H0YMB1, H0YNE5

UniProt curated annotations — full annotation on UniProt →

Function. Involved in cellular calcium homeostasis regulation. May participate in differentiation and apoptosis of keratinocytes. Overexpression induces apoptosis.

Subunit / interactions. Interacts with PTPN2. Interacts with microtubules. Interacts with VAPB. Interacts (via FFAT motif) with MOSPD2 (via MSP domain). Interacts (via phosphorylated FFAT motif) with MOSPD2, VAPA and VAPB.

Subcellular location. Mitochondrion outer membrane. Cytoplasm. Nucleus. Cytoskeleton. Spindle. Spindle pole.

Tissue specificity. Present at high level in epidermis and seminiferous epithelium: while basal cells in the epidermis and spermatogonia show no perceptible amount, keratinocytes of suprabasal layers and differentiating first-order spermatocytes up to spermatids exhibit high expression. In skeletal muscle, its presence is restricted to fibers of the fast twitch type. In surface epithelia containing ciliated cells, it is associated with the microtubular structures responsible for ciliary movement. Also present in specific structures of the central nervous system such as neurons of the hippocampal region, ganglion cells of the autonomic nervous system, and axons of the peripheral nervous system (at protein level). Widely expressed.

Post-translational modifications. Phosphorylation at Thr-160 of the FFAT motif activates interaction with MOSPD2, VAPA and VAPB.

Domain organisation. The transmembrane region is required for mitochondrial localization. The FFAT motif is required for interaction with MOSPD2. The FFAT motif is involved in the interaction with VAPA and VAPB and its phosphorylation regulates these interactions.

Induction. By EGF, TGFB1, retinoic acid- and 1,25-dihydroxyvitamin D(3).

Similarity. Belongs to the RMDN family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96TC7-1	1	yes
Q96TC7-2	2

RefSeq proteins (6): NP_001291731, NP_001310823, NP_001310824, NP_001310825, NP_001310826, NP_060615* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR049039

Pfam: PF21033

UniProt features (37 total): helix 14, modified residue 9, topological domain 2, sequence conflict 2, compositionally biased region 2, chain 1, splice variant 1, sequence variant 1, transmembrane region 1, mutagenesis site 1, region of interest 1, coiled-coil region 1, short sequence motif 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
7CC7	X-RAY DIFFRACTION	1.45

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96TC7-F1	73.48	0.46

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 (9): 46, 50, 57, 160, 183, 193, 212, 232, 44

Mutagenesis-validated functional residues (1):

Position	Phenotype
157–172	reduces interaction with mospd2.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 217 (showing top): GCM_MAP4K4, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GCM_GSPT1, FOSTER_TOLERANT_MACROPHAGE_UP, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, MODULE_256, MODULE_480, GOCC_MITOCHONDRIAL_ENVELOPE, SANSOM_APC_TARGETS_DN, GOBP_MONOATOMIC_ION_HOMEOSTASIS, GCM_NF2, GCM_CALM1, BURTON_ADIPOGENESIS_5, MODULE_333, MODULE_427

GO Biological Process (3): intracellular calcium ion homeostasis (GO:0006874), apoptotic process (GO:0006915), cell differentiation (GO:0030154)

GO Molecular Function (2): microtubule binding (GO:0008017), protein binding (GO:0005515)

GO Cellular Component (16): nucleus (GO:0005634), cytoplasm (GO:0005737), mitochondrion (GO:0005739), mitochondrial outer membrane (GO:0005741), spindle microtubule (GO:0005876), organelle membrane contact site (GO:0044232), intercellular bridge (GO:0045171), mitotic spindle pole (GO:0097431), presynapse (GO:0098793), postsynapse (GO:0098794), glutamatergic synapse (GO:0098978), spindle pole (GO:0000922), spindle (GO:0005819), cytoskeleton (GO:0005856), microtubule (GO:0005874), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	7
synapse	3
intracellular membrane-bounded organelle	2
spindle	2
microtubule cytoskeleton	2
intracellular membraneless organelle	2
intracellular monoatomic cation homeostasis	1
calcium ion homeostasis	1
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
cellular developmental process	1
tubulin binding	1
binding	1
intracellular anatomical structure	1
cytoplasm	1
mitochondrial membrane	1
organelle outer membrane	1
microtubule	1
organelle	1
spindle pole	1
mitotic spindle	1
polymeric cytoskeletal fiber	1

Protein interactions and networks

STRING

2068 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RMDN3	VAPB	O95292	997
RMDN3	OSBPL5	Q9H0X9	991
RMDN3	OSBPL8	Q9BZF1	989
RMDN3	PTPN1	P18031	908
RMDN3	MFN2	O95140	899
RMDN3	MOSPD2	Q8NHP6	898
RMDN3	P3H3	Q8IVL6	837
RMDN3	KCNIP1	Q9NZI2	823
RMDN3	PACS2	Q86VP3	821
RMDN3	BCAP31	P51572	820
RMDN3	FIS1	Q9Y3D6	806
RMDN3	ITPR3	Q14573	778
RMDN3	PTPN2	P17706	763
RMDN3	VDAC1	P21796	752
RMDN3	RTRAF	Q9Y224	730

IntAct

197 interactions, top by confidence:

A	B	Type	Score
YWHAB	RMDN3	psi-mi:“MI:0915”(physical association)	0.820
RMDN3	YWHAB	psi-mi:“MI:0914”(association)	0.820
YWHAB	RMDN3	psi-mi:“MI:0403”(colocalization)	0.820
YWHAB	RMDN3	psi-mi:“MI:2364”(proximity)	0.820
RMDN3	YWHAB	psi-mi:“MI:2364”(proximity)	0.820
RMDN3	VAPA	psi-mi:“MI:0915”(physical association)	0.800
RMDN3	YWHAG	psi-mi:“MI:0915”(physical association)	0.760
YWHAG	RMDN3	psi-mi:“MI:0914”(association)	0.760
VAPB	FAM83G	psi-mi:“MI:0914”(association)	0.730
B3GNT3	PGRMC1	psi-mi:“MI:0914”(association)	0.670
NEUROG3	GXYLT2	psi-mi:“MI:0914”(association)	0.640
VAPA	FAM83G	psi-mi:“MI:0914”(association)	0.640
TRDN	TMEM223	psi-mi:“MI:0914”(association)	0.640
VAPA	PITPNM1	psi-mi:“MI:0914”(association)	0.640
NIPAL1	ESYT2	psi-mi:“MI:0914”(association)	0.640
RMDN2	RMDN3	psi-mi:“MI:0915”(physical association)	0.590
PTPN1	RMDN3	psi-mi:“MI:0403”(colocalization)	0.570
RMDN3	PTPN1	psi-mi:“MI:2364”(proximity)	0.570
PTPN1	RMDN3	psi-mi:“MI:2364”(proximity)	0.570

BioGRID (400): RMDN3 (Affinity Capture-MS), RMDN3 (Affinity Capture-MS), RMDN3 (Affinity Capture-MS), RMDN3 (Affinity Capture-MS), RMDN3 (Affinity Capture-MS), RMDN3 (Affinity Capture-MS), RMDN3 (Affinity Capture-MS), RMDN3 (Affinity Capture-MS), RMDN3 (Affinity Capture-MS), RMDN3 (Affinity Capture-MS), RMDN3 (Affinity Capture-MS), RMDN3 (Affinity Capture-MS), RMDN3 (Affinity Capture-MS), RMDN3 (Affinity Capture-MS), RMDN3 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I6ASZ5, A0JN53, A4IG66, D3Z8X7, D3ZND0, G3X992, O00750, O08836, O70576, P0DKR2, Q15021, Q1JQC5, Q1L5Z9, Q1LWH4, Q1LXZ7, Q2YD98, Q3T1I9, Q3TV65, Q3UJU9, Q4R5Q4, Q5EAU9, Q5JTW2, Q5R6Z1, Q5TC12, Q61249, Q66H15, Q6NY52, Q6P5E6, Q6PBQ2, Q6PI26, Q80TE0, Q80V31, Q80XC6, Q8BIW9, Q8BM55, Q8K2Z4, Q8R3L2, Q8VDP4, Q8WVB6, Q92574

Diamond homologs: P34560, Q0P4W3, Q1JQC5, Q2TBQ7, Q32KL4, Q3UJU9, Q498D5, Q4G069, Q5EAU9, Q5R6Z1, Q5R8E4, Q66H15, Q8BSE0, Q95LL7, Q96DB5, Q96LZ7, Q96TC7, Q9DCV4

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
RMDN3	“form complex”	“VAPB-PTPIP51 complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 169 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.

GO biological processes:

GO term	Partners	Fold	FDR
zinc ion transmembrane transport	5	23.6×	5e-04
intracellular zinc ion homeostasis	6	19.4×	3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	60
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
585332	GRCh37/hg19 15q14-15.1 chr15:34638237..42057083 complex variant	Pathogenic

SpliceAI

2304 predictions. Top by Δscore:

Variant	Effect	Δscore
15:40737125:T:TA	donor_gain	1.0000
15:40737203:CA:C	acceptor_gain	1.0000
15:40737205:C:CC	acceptor_gain	1.0000
15:40737306:T:TA	donor_gain	1.0000
15:40737342:C:CA	acceptor_loss	1.0000
15:40737342:C:CC	acceptor_gain	1.0000
15:40737343:T:A	acceptor_loss	1.0000
15:40737723:AGACC:A	acceptor_loss	1.0000
15:40737726:CCT:C	acceptor_loss	1.0000
15:40737727:C:CG	acceptor_loss	1.0000
15:40737728:T:A	acceptor_loss	1.0000
15:40738040:CTC:C	acceptor_gain	1.0000
15:40738043:C:CC	acceptor_gain	1.0000
15:40738043:CTA:C	acceptor_loss	1.0000
15:40738044:T:G	acceptor_loss	1.0000
15:40738495:CCTCA:C	donor_loss	1.0000
15:40738496:CTCAC:C	donor_loss	1.0000
15:40738497:TCAC:T	donor_loss	1.0000
15:40738498:CA:C	donor_loss	1.0000
15:40738499:A:T	donor_loss	1.0000
15:40738500:C:G	donor_loss	1.0000
15:40738577:CT:C	acceptor_loss	1.0000
15:40744046:CCAT:C	donor_gain	1.0000
15:40744145:CCATA:C	acceptor_gain	1.0000
15:40744146:CATA:C	acceptor_gain	1.0000
15:40744146:CATAC:C	acceptor_gain	1.0000
15:40744148:TA:T	acceptor_gain	1.0000
15:40744150:C:CC	acceptor_gain	1.0000
15:40744976:CCA:C	donor_gain	1.0000
15:40745257:TAA:T	acceptor_gain	1.0000

AlphaMissense

3033 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:40738571:G:T	A326E	0.991
15:40744112:C:G	R282P	0.991
15:40737976:A:G	W372R	0.990
15:40737976:A:T	W372R	0.990
15:40737981:C:T	G370D	0.990
15:40744110:C:G	A283P	0.989
15:40738027:C:G	A355P	0.987
15:40740193:C:T	G304E	0.986
15:40737202:G:C	C427W	0.985
15:40737982:C:G	G370R	0.985
15:40738572:C:G	A326P	0.985
15:40740182:C:G	A308P	0.985
15:40737204:A:G	C427R	0.984
15:40744118:A:G	L280P	0.983
15:40744121:C:G	R279P	0.983
15:40737648:C:G	A402P	0.982
15:40744115:G:T	A281D	0.982
15:40744996:A:G	L263P	0.981
15:40738501:C:A	K349N	0.980
15:40738501:C:G	K349N	0.980
15:40744122:G:T	R279S	0.979
15:40744047:C:G	G304R	0.978
15:40744047:C:T	G304R	0.978
15:40737644:A:G	L403P	0.977
15:40737647:G:T	A402D	0.975
15:40737981:C:A	G370V	0.975
15:40751434:A:C	S172R	0.975
15:40751434:A:T	S172R	0.975
15:40751436:T:G	S172R	0.975
15:40751473:G:C	F159L	0.975

dbSNP variants (sampled 300 via entrez): RS1000116151 (15:40755005 A>G), RS1000117066 (15:40747654 G>A), RS1000138261 (15:40737505 G>A,C,T), RS1000269920 (15:40742307 C>T), RS1000743649 (15:40749195 G>A), RS1000867394 (15:40737162 TC>T), RS1000950459 (15:40744791 G>A), RS1000958993 (15:40744532 A>G), RS1001070524 (15:40746361 A>C), RS1001090732 (15:40739237 C>T), RS1001114844 (15:40755746 T>A), RS1001166955 (15:40755539 C>A,T), RS1001344259 (15:40750434 G>A,C), RS1001543236 (15:40738989 A>C), RS1001735542 (15:40737806 T>G)

Disease associations

OMIM: gene MIM:611873 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): spindle cell sarcoma (MONDO:0002927)

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST008559_8	Anxiety and stress-related disorders	7.000000e-07
GCST010002_167	Refractive error	3.000000e-11
GCST010725_23	Malaria	2.000000e-06
GCST010725_38	Malaria	3.000000e-06
GCST010725_80	Malaria	7.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010098	stress-related disorder

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases methylation, decreases expression, increases expression, affects cotreatment	3
Valproic Acid	affects expression, increases expression, increases methylation	3
FR900359	increases phosphorylation	1
2,4,6-tribromophenol	increases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	affects expression	1
beta-lapachone	decreases expression	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
tetrabromobisphenol A	increases expression	1
perfluorooctanoic acid	increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
efavirenz	increases expression	1
ICG 001	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
pentabrominated diphenyl ether 100	increases expression	1
hexabrominated diphenyl ether 153	increases expression	1
bisphenol S	affects expression	1
bisphenol AF	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	increases expression	1
Arsenic	increases expression, affects cotreatment, increases abundance	1
Caffeine	decreases phosphorylation	1
Ivermectin	decreases expression	1
Lead	decreases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Phenolsulfonphthalein	affects cotreatment, increases expression	1
Smoke	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2DW	Abcam HeLa RMDN3 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04906876	PHASE2	WITHDRAWN	A Phase 2 Study of 9-ING-41Combined With Chemotherapy in Adolescents and Adults With Advanced Sarcomas
NCT05116800	PHASE2	WITHDRAWN	Phase 2 Study of 9-ING-41 With Chemotherapy in Sarcoma
NCT04420975	PHASE1	ACTIVE_NOT_RECRUITING	Nivolumab and BO-112 Before Surgery for the Treatment of Resectable Soft Tissue Sarcoma
NCT03874455	Not specified	NO_LONGER_AVAILABLE	Tazemetostat Expanded Access Program for Adults With Solid Tumors
NCT05974410	Not specified	AVAILABLE	Expanded Access to Immunomodulatory AVM0703 for Solid Tumor and Blood Cancer Patients
NCT06526897	Not specified	NOT_YET_RECRUITING	Evaluation of Chest CT Versus Chest X-Ray for Lung Surveillance After Curative-Intent Resection of High-Risk Truncal-Extremity Soft Tissue Sarcoma