RMDN1

Summary

RMDN1 (regulator of microtubule dynamics 1, HGNC:24285) is a protein-coding gene on chromosome 8q21.3, encoding Regulator of microtubule dynamics protein 1 (Q96DB5).

Enables microtubule binding activity. Predicted to be involved in attachment of mitotic spindle microtubules to kinetochore and mitotic spindle organization. Located in mitotic spindle pole and spindle microtubule.

Source: NCBI Gene 51115 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 50 total
• MANE Select transcript: NM_016033

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24285
Approved symbol	RMDN1
Name	regulator of microtubule dynamics 1
Location	8q21.3
Locus type	gene with protein product
Status	Approved
Aliases	CGI-90, FLJ20665, RMD1
Ensembl gene	ENSG00000176623
Ensembl biotype	protein_coding
OMIM	611871
Entrez	51115

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 19 protein_coding, 4 retained_intron, 3 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000406452, ENST00000430676, ENST00000517404, ENST00000517710, ENST00000517821, ENST00000518390, ENST00000518772, ENST00000519145, ENST00000519247, ENST00000519639, ENST00000519789, ENST00000519966, ENST00000520719, ENST00000521045, ENST00000522804, ENST00000522942, ENST00000523370, ENST00000523911, ENST00000524172, ENST00000902719, ENST00000902720, ENST00000902721, ENST00000902722, ENST00000902723, ENST00000949087, ENST00000949088, ENST00000949089

RefSeq mRNA: 4 — MANE Select: NM_016033 NM_001286707, NM_001286719, NM_001317807, NM_016033

CCDS: CCDS34918, CCDS69509, CCDS69510, CCDS83305

Canonical transcript exons

ENST00000406452 — 10 exons

Exon	Start	End
ENSE00001289651	86508492	86508686
ENSE00001756516	86477294	86477324
ENSE00001782437	86478923	86479010
ENSE00002096442	86472349	86474358
ENSE00003466803	86488552	86488639
ENSE00003582079	86480277	86480332
ENSE00003586379	86506995	86507112
ENSE00003616877	86484872	86484961
ENSE00003637811	86486484	86486643
ENSE00003689877	86474820	86474953

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 96.90.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 40.0785 / max 193.3241, expressed in 1821 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
93816	36.4279	1821
93818	1.8456	1158
93817	1.0296	765
93820	0.7141	350
93819	0.0612	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	96.90	gold quality
tendon	UBERON:0000043	96.51	gold quality
adrenal tissue	UBERON:0018303	96.41	gold quality
right lobe of thyroid gland	UBERON:0001119	96.19	gold quality
left lobe of thyroid gland	UBERON:0001120	96.04	gold quality
mucosa of stomach	UBERON:0001199	96.01	gold quality
tibial nerve	UBERON:0001323	96.00	gold quality
rectum	UBERON:0001052	95.92	gold quality
right lobe of liver	UBERON:0001114	95.86	gold quality
tendon of biceps brachii	UBERON:0008188	95.82	gold quality
gastrocnemius	UBERON:0001388	95.80	gold quality
heart left ventricle	UBERON:0002084	95.76	gold quality
muscle of leg	UBERON:0001383	95.75	gold quality
cardiac ventricle	UBERON:0002082	95.62	gold quality
heart right ventricle	UBERON:0002080	95.56	gold quality
thyroid gland	UBERON:0002046	95.51	gold quality
right atrium auricular region	UBERON:0006631	95.41	gold quality
metanephros cortex	UBERON:0010533	95.11	gold quality
right adrenal gland cortex	UBERON:0035827	95.03	gold quality
heart	UBERON:0000948	94.92	gold quality
hindlimb stylopod muscle	UBERON:0004252	94.88	gold quality
right adrenal gland	UBERON:0001233	94.75	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	94.66	gold quality
cardiac atrium	UBERON:0002081	94.43	gold quality
lower esophagus	UBERON:0013473	94.40	gold quality
lower esophagus muscularis layer	UBERON:0035833	94.39	gold quality
small intestine Peyer’s patch	UBERON:0003454	94.36	gold quality
esophagus mucosa	UBERON:0002469	94.24	gold quality
muscle layer of sigmoid colon	UBERON:0035805	94.23	gold quality
esophagus	UBERON:0001043	94.21	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

55 targeting RMDN1, 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-3613-3P	100.00	76.36	7965
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-4420	99.82	70.08	1624
HSA-MIR-181B-2-3P	99.81	70.06	1646
HSA-MIR-181B-3P	99.81	70.06	1646
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-4502	99.65	66.99	1021
HSA-MIR-5003-5P	99.61	69.13	1624
HSA-MIR-3942-3P	99.57	69.03	2854
HSA-MIR-5695	99.41	67.48	1047
HSA-MIR-3160-5P	99.28	69.07	1938
HSA-MIR-548AS-3P	99.12	69.12	2294

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rmdn1	ENSDARG00000074507
mus_musculus	Rmdn1	ENSMUSG00000028229
rattus_norvegicus	Rmdn1	ENSRNOG00000025145
caenorhabditis_elegans	F33H2.6	WBGENE00009369

Paralogs (3): RMDN2 (ENSG00000115841), TEX10 (ENSG00000136891), RMDN3 (ENSG00000137824)

Protein

Protein identifiers

Regulator of microtubule dynamics protein 1 — Q96DB5 (reviewed: Q96DB5)

Alternative names: Protein FAM82B

All UniProt accessions (12): Q96DB5, E5RGC8, E5RH53, E5RJC7, E5RJV0, E7EWZ7, H0YAP5, H0YB03, H0YB83, H0YBD9, H0YC27, H0YC67

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with microtubules.

Subcellular location. Cytoplasm. Cytoskeleton. Spindle. Spindle pole.

Similarity. Belongs to the RMDN family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q96DB5-1	1	yes
Q96DB5-2	2
Q96DB5-3	3

RefSeq proteins (4): NP_001273636, NP_001273648, NP_001304736, NP_057117* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR049039

Pfam: PF21033

UniProt features (9 total): repeat 2, splice variant 2, sequence conflict 2, chain 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96DB5-F1	84.49	0.71

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 (1): 165

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 144 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, GOBP_CHROMOSOME_ORGANIZATION, GOBP_ATTACHMENT_OF_SPINDLE_MICROTUBULES_TO_KINETOCHORE, GOBP_CHROMOSOME_LOCALIZATION, MATTIOLI_MGUS_VS_PCL, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, GOCC_MICROTUBULE_ORGANIZING_CENTER, ONKEN_UVEAL_MELANOMA_UP, GOBP_ORGANELLE_FISSION, GOCC_CENTROSOME, GOBP_MITOTIC_NUCLEAR_DIVISION, GOBP_MITOTIC_CELL_CYCLE, CUI_TCF21_TARGETS_2_DN, ACEVEDO_LIVER_CANCER_UP, GOBP_ORGANELLE_LOCALIZATION

GO Biological Process (2): mitotic spindle organization (GO:0007052), attachment of mitotic spindle microtubules to kinetochore (GO:0051315)

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

GO Cellular Component (8): cytoplasm (GO:0005737), mitochondrion (GO:0005739), spindle microtubule (GO:0005876), mitotic spindle pole (GO:0097431), spindle pole (GO:0000922), spindle (GO:0005819), cytoskeleton (GO:0005856), microtubule (GO:0005874)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
spindle	2
microtubule cytoskeleton	2
intracellular membraneless organelle	2
mitotic cell cycle	1
spindle organization	1
microtubule cytoskeleton organization involved in mitosis	1
mitotic metaphase chromosome alignment	1
attachment of spindle microtubules to kinetochore	1
mitotic cell cycle process	1
tubulin binding	1
binding	1
intracellular anatomical structure	1
cytoplasm	1
intracellular membrane-bounded organelle	1
microtubule	1
spindle pole	1
mitotic spindle	1
polymeric cytoskeletal fiber	1

Protein interactions and networks

STRING

1660 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RMDN1	ARMC1	Q9NVT9	550
RMDN1	PTPN2	P17706	546
RMDN1	MRPL13	Q9BYD1	510
RMDN1	TMEM70	Q9BUB7	501
RMDN1	VCPIP1	Q96JH7	496
RMDN1	FAM91A1	Q658Y4	479
RMDN1	RRS1	Q15050	475
RMDN1	AURKB	Q96GD4	458
RMDN1	ELOC	Q15369	437
RMDN1	PTPN1	P18031	428
RMDN1	PARP1	P09874	424
RMDN1	UBE2V2	Q15819	416
RMDN1	TIGD5	Q53EQ6	414
RMDN1	PGBD4	Q96DM1	399
RMDN1	CPNE3	O75131	375

IntAct

37 interactions, top by confidence:

A	B	Type	Score
SUZ12	EED	psi-mi:“MI:0914”(association)	0.910
HRAS	MTHFD2	psi-mi:“MI:0914”(association)	0.730
NRAS	RGL2	psi-mi:“MI:0914”(association)	0.550
CYP2E1	RMDN1	psi-mi:“MI:0914”(association)	0.530
RMDN1	LUM	psi-mi:“MI:0915”(physical association)	0.400
Myh9	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
CDK2	BLTP3B	psi-mi:“MI:0914”(association)	0.350
Junb	RGPD3	psi-mi:“MI:0914”(association)	0.350
CHIT1	VHL	psi-mi:“MI:0914”(association)	0.350
H2AX	ANXA6	psi-mi:“MI:0914”(association)	0.350
HTRA4	PSMD12	psi-mi:“MI:0914”(association)	0.350
DDB1	POLRMT	psi-mi:“MI:0914”(association)	0.350
SAR1B	UBA6	psi-mi:“MI:0914”(association)	0.350
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
S100P	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
S100A6	VWA8	psi-mi:“MI:0914”(association)	0.350
CENPM	DNM1L	psi-mi:“MI:0914”(association)	0.350
TOP3B	PRMT5	psi-mi:“MI:0914”(association)	0.350
CHIT1	SMAD7	psi-mi:“MI:0914”(association)	0.350
NIPA2	SYNGR2	psi-mi:“MI:0914”(association)	0.350
ANLN	UBA6	psi-mi:“MI:0914”(association)	0.350
SERBP1	UBA6	psi-mi:“MI:0914”(association)	0.350
NTNG1	UBA6	psi-mi:“MI:0914”(association)	0.350
WIF1	SMCHD1	psi-mi:“MI:0914”(association)	0.350
SYT6	SUPT5H	psi-mi:“MI:0914”(association)	0.350
XPA	ENSA	psi-mi:“MI:0914”(association)	0.350
CABCOCO1	NARS1	psi-mi:“MI:0914”(association)	0.350
PDLIM5	ZMPSTE24	psi-mi:“MI:0914”(association)	0.350
PAQR3	AGFG1	psi-mi:“MI:0914”(association)	0.350

BioGRID (60): RMDN1 (Co-fractionation), SHC1 (Co-fractionation), RMDN1 (Synthetic Growth Defect), RMDN1 (Affinity Capture-MS), RMDN1 (Affinity Capture-MS), RMDN1 (Affinity Capture-MS), RMDN1 (Affinity Capture-MS), RMDN1 (Affinity Capture-MS), RMDN1 (Affinity Capture-MS), RMDN1 (Proximity Label-MS), RMDN1 (Proximity Label-MS), SUZ12 (Affinity Capture-MS), EED (Affinity Capture-MS), RMDN1 (Affinity Capture-MS), EZH2 (Affinity Capture-MS)

ESM2 similar proteins: A1A4L1, A4QP75, B0S6U7, E1BPN0, E7FCP8, O00142, O55171, P0C1Q3, P19686, P19687, P33402, P49753, P57075, Q02108, Q08CH3, Q1L5Z9, Q1LWG4, Q3B8B2, Q3SZV6, Q3UUI3, Q4V8A1, Q4ZHS0, Q502J0, Q566R0, Q58CX2, Q5IRJ6, Q5R4H0, Q5R8E4, Q5SY16, Q5ZIU8, Q60963, Q63159, Q66GI4, Q6GLK2, Q6PML9, Q6TEC1, Q810S1, Q8BMS4, Q8BWM0, Q8N159

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	36
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2459 predictions. Top by Δscore:

Variant	Effect	Δscore
8:86474815:TTTA:T	donor_loss	1.0000
8:86474817:TACC:T	donor_loss	1.0000
8:86474819:CC:C	donor_loss	1.0000
8:86474954:C:CC	acceptor_gain	1.0000
8:86486479:CTCA:C	donor_loss	1.0000
8:86486480:TCACC:T	donor_loss	1.0000
8:86486482:A:AC	donor_gain	1.0000
8:86486482:A:AT	donor_loss	1.0000
8:86486482:AC:A	donor_gain	1.0000
8:86486483:C:CC	donor_gain	1.0000
8:86486483:CC:C	donor_gain	1.0000
8:86486483:CCTT:C	donor_gain	1.0000
8:86486639:CTTCA:C	acceptor_gain	1.0000
8:86486640:TTCA:T	acceptor_gain	1.0000
8:86486641:TCA:T	acceptor_gain	1.0000
8:86486642:CA:C	acceptor_gain	1.0000
8:86486642:CAC:C	acceptor_gain	1.0000
8:86486643:ACTA:A	acceptor_loss	1.0000
8:86486644:C:CC	acceptor_gain	1.0000
8:86486647:A:AC	acceptor_gain	1.0000
8:86486647:A:C	acceptor_gain	1.0000
8:86486648:T:C	acceptor_gain	1.0000
8:86486648:T:TC	acceptor_gain	1.0000
8:86486649:T:C	acceptor_gain	1.0000
8:86486649:T:TC	acceptor_gain	1.0000
8:86486654:A:AC	acceptor_gain	1.0000
8:86486654:A:C	acceptor_gain	1.0000
8:86488546:GCTT:G	donor_loss	1.0000
8:86488547:CTTAC:C	donor_loss	1.0000
8:86488548:TTACC:T	donor_loss	1.0000

AlphaMissense

2034 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:86480329:C:G	A197P	0.997
8:86484954:G:T	A168E	0.997
8:86484961:A:G	W166R	0.997
8:86484961:A:T	W166R	0.997
8:86480284:C:G	G212R	0.996
8:86474866:A:G	L283P	0.995
8:86486611:C:G	R123P	0.995
8:86474914:C:T	G267E	0.994
8:86474915:C:G	G267R	0.994
8:86474915:C:T	G267R	0.994
8:86474928:G:C	N262K	0.994
8:86474928:G:T	N262K	0.994
8:86480289:A:G	L210P	0.994
8:86486620:C:G	R120P	0.994
8:86486621:G:T	R120S	0.994
8:86477303:C:G	A251P	0.993
8:86480278:A:G	W214R	0.993
8:86480278:A:T	W214R	0.993
8:86480283:C:T	G212D	0.993
8:86486602:C:G	R126P	0.993
8:86486624:A:G	W119R	0.993
8:86486624:A:T	W119R	0.993
8:86488619:C:G	A90P	0.993
8:86474940:G:C	F258L	0.992
8:86474940:G:T	F258L	0.992
8:86474942:A:G	F258L	0.992
8:86486484:C:A	K165N	0.992
8:86486484:C:G	K165N	0.992
8:86486522:C:G	A153P	0.992
8:86484955:C:G	A168P	0.991

dbSNP variants (sampled 300 via entrez): RS1000210785 (8:86509157 G>T), RS1000245737 (8:86504532 A>G), RS1000256821 (8:86481062 A>G), RS1000286794 (8:86512443 T>C), RS1000299350 (8:86504278 C>G,T), RS1000307787 (8:86481432 G>T), RS1000390297 (8:86505758 C>T), RS1000445000 (8:86512051 GTGAA>G), RS1000542052 (8:86498866 C>T), RS1000620857 (8:86510928 A>C), RS1000643471 (8:86479858 G>C), RS1000750690 (8:86472803 C>A,T), RS1000776512 (8:86510641 C>G), RS1000821257 (8:86474148 C>G,T), RS1000846173 (8:86476240 T>A)

Disease associations

OMIM: gene MIM:611871 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST005316_88	Intelligence (MTAG)	2.000000e-08
GCST006585_371	Blood protein levels	5.000000e-313

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	3
bisphenol F	increases expression, affects cotreatment	2
bisphenol A	decreases expression, affects cotreatment, increases expression	2
Aflatoxin B1	decreases methylation, increases methylation	2
GSK-J4	decreases expression	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenate	decreases expression	1
beta-lapachone	increases expression	1
methylparaben	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cobaltous chloride	decreases expression	1
perfluorooctanoic acid	increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
aflatoxin B2	decreases methylation	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
bisphenol B	increases expression	1
bisphenol S	increases expression	1
bisphenol AF	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Vorinostat	increases expression	1
Acetaminophen	decreases expression	1
Cadmium	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Rotenone	decreases expression	1

Clinical trials (associated diseases)

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