MTCL1

Summary

MTCL1 (microtubule crosslinking factor 1, HGNC:29121) is a protein-coding gene on chromosome 18p11.22, encoding Microtubule cross-linking factor 1 (Q9Y4B5). Microtubule-associated factor involved in the late phase of epithelial polarization and microtubule dynamics regulation.

Enables microtubule binding activity. Involved in chromosome segregation. Located in kinetochore; midbody; and spindle.

Source: NCBI Gene 23255 — RefSeq curated summary.

At a glance

• Gene–disease (curated): hereditary neurological disease (Strong, GenCC)
• GWAS associations: 13
• Clinical variants (ClinVar): 368 total — 1 pathogenic
• MANE Select transcript: NM_001395333

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29121
Approved symbol	MTCL1
Name	microtubule crosslinking factor 1
Location	18p11.22
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000168502
Ensembl biotype	protein_coding
OMIM	615766
Entrez	23255

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 10 protein_coding, 7 protein_coding_CDS_not_defined, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000306329, ENST00000359865, ENST00000517554, ENST00000517570, ENST00000518226, ENST00000518815, ENST00000519823, ENST00000520495, ENST00000520926, ENST00000521018, ENST00000522146, ENST00000522592, ENST00000523122, ENST00000523811, ENST00000581670, ENST00000695635, ENST00000695636, ENST00000911530, ENST00000911531, ENST00000911532, ENST00000911533

RefSeq mRNA: 6 — MANE Select: NM_001395333 NM_001378205, NM_001378206, NM_001378207, NM_001395220, NM_001395333, NM_015210

CCDS: CCDS11841, CCDS92431, CCDS92432, CCDS92433, CCDS92434

Canonical transcript exons

ENST00000695636 — 15 exons

Exon	Start	End
ENSE00003964536	8785936	8786091
ENSE00003964537	8818963	8819259
ENSE00003964538	8777833	8777892
ENSE00003964539	8796232	8796462
ENSE00003964540	8798097	8798291
ENSE00003964541	8705556	8706713
ENSE00003964542	8792998	8793120
ENSE00003964543	8806893	8807060
ENSE00003964544	8718424	8718648
ENSE00003964545	8812979	8813233
ENSE00003964547	8783530	8784843
ENSE00003964548	8720338	8720496
ENSE00003964549	8831607	8832778
ENSE00003964550	8821467	8821498
ENSE00003964551	8824699	8826232

Expression profiles

Bgee: expression breadth ubiquitous, 236 present calls, max score 98.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.5883 / max 240.6264, expressed in 1439 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
169306	2.7886	1164
169308	1.7508	910
169307	0.9982	606
169305	0.4863	265
169304	0.4158	192
169316	0.0782	30
169315	0.0447	4
169309	0.0163	5
169310	0.0093	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar cortex	UBERON:0002129	98.99	gold quality
cerebellar hemisphere	UBERON:0002245	98.98	gold quality
cerebellum	UBERON:0002037	98.96	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.60	gold quality
cerebellar vermis	UBERON:0004720	97.53	gold quality
middle temporal gyrus	UBERON:0002771	94.48	gold quality
muscle layer of sigmoid colon	UBERON:0035805	93.49	gold quality
hair follicle	UBERON:0002073	92.38	gold quality
Brodmann (1909) area 23	UBERON:0013554	92.11	gold quality
primary visual cortex	UBERON:0002436	91.66	gold quality
pigmented layer of retina	UBERON:0001782	91.39	gold quality
retina	UBERON:0000966	91.36	gold quality
adult organism	UBERON:0007023	90.99	gold quality
endothelial cell	CL:0000115	90.79	gold quality
gall bladder	UBERON:0002110	88.10	gold quality
colonic epithelium	UBERON:0000397	88.03	gold quality
gingival epithelium	UBERON:0001949	87.77	gold quality
stromal cell of endometrium	CL:0002255	87.68	gold quality
tibia	UBERON:0000979	87.67	gold quality
lower esophagus muscularis layer	UBERON:0035833	87.39	gold quality
gingiva	UBERON:0001828	87.36	gold quality
lower esophagus	UBERON:0013473	87.34	gold quality
Brodmann (1909) area 46	UBERON:0006483	87.31	gold quality
sural nerve	UBERON:0015488	87.11	gold quality
urinary bladder	UBERON:0001255	86.90	gold quality
pancreatic ductal cell	CL:0002079	86.44	gold quality
ganglionic eminence	UBERON:0004023	86.23	gold quality
mucosa of stomach	UBERON:0001199	86.21	gold quality
right testis	UBERON:0004534	85.87	gold quality
left testis	UBERON:0004533	85.42	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)

113 targeting MTCL1, 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-1277-5P	100.00	73.95	5056
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-8082	99.95	67.27	1170
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-101-3P	99.94	75.03	2230
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838

Literature-anchored findings (GeneRIF, showing 6)

• MTCL1 cooperates with CLASPs and AKAP450/CG-NAP in the formation of the Golgi-derived microtubules (PMID:25366663)
• results suggest that the PPP2R5E phosphatase may contribute to microtubule organization by stabilizing MTCL1. (PMID:27521566)
• microtubule-regulating activity of microtubule crosslinking factor 1 (PMID:28787032)
• We propose MTCL1 as a candidate gene for autosomal recessive cerebellar ataxia in humans. In addition, our study confirms the high diagnostic yield of NGS in early-onset cerebellar ataxias, with at least 50% detection rate in our ataxia cohort. (PMID:30548255)
• SOGA1 and SOGA2/MTCL1 are CLASP-interacting proteins required for faithful chromosome segregation in human cells. (PMID:33587225)
• Circular RNA MTCL1 targets SMAD3 by sponging miR-145-5p for regulation of cell proliferation and migration in Hirschsprung’s disease. (PMID:38127107)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	mtcl1	ENSDARG00000091408
mus_musculus	Mtcl1	ENSMUSG00000052105
rattus_norvegicus	Mtcl1	ENSRNOG00000025527

Paralogs (2): MTCL2 (ENSG00000149639), MTCL3 (ENSG00000214338)

Protein

Protein identifiers

Microtubule cross-linking factor 1 — Q9Y4B5 (reviewed: Q9Y4B5)

Alternative names: Coiled-coil domain-containing protein 165, PAR-1-interacting protein, SOGA family member 2

All UniProt accessions (5): Q9Y4B5, A0A8Q3SIW6, A0A8Q3WKN6, J3QL92, J3QLE1

UniProt curated annotations — full annotation on UniProt →

Function. Microtubule-associated factor involved in the late phase of epithelial polarization and microtubule dynamics regulation. Plays a role in the development and maintenance of non-centrosomal microtubule bundles at the lateral membrane in polarized epithelial cells. Required for faithful chromosome segregation during mitosis.

Subunit / interactions. Homodimer. Associates (via N- and C-terminus domains) with microtubule filaments. Interacts with MARK2; the interaction is direct.

Subcellular location. Lateral cell membrane. Apical cell membrane. Cytoplasm. Cytoskeleton. Spindle pole. Midbody.

Post-translational modifications. Phosphorylated during mitosis in a CDK1-dependent manner.

Similarity. Belongs to the SOGA family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9Y4B5-1	1	yes
Q9Y4B5-2	2
Q9Y4B5-3	3
Q9Y4B5-4	4

RefSeq proteins (6): NP_001365134, NP_001365135, NP_001365136, NP_001382149, NP_001382262, NP_056025 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027881	SOGA_CC	Domain
IPR027882	SOGA1/2-like_CC	Domain
IPR049885	MTCL1-3	Family

Pfam: PF11365, PF14818

UniProt features (82 total): modified residue 36, region of interest 18, compositionally biased region 11, splice variant 6, coiled-coil region 5, sequence variant 5, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y4B5-F1	51.33	0.06

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 (36): 77, 87, 217, 221, 263, 549, 618, 621, 685, 776, 901, 923, 1278, 1385, 1388, 1399, 1417, 1421, 1427, 1514 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 200 (showing top): MULLIGHAN_NPM1_SIGNATURE_3_UP, GOBP_REGULATION_OF_AUTOPHAGY, GOBP_ESTABLISHMENT_OR_MAINTENANCE_OF_CELL_POLARITY, LU_IL4_SIGNALING, GOBP_PROTEIN_TARGETING, GOBP_REGULATION_OF_PROTEIN_TARGETING_TO_MEMBRANE, BILD_HRAS_ONCOGENIC_SIGNATURE, GOBP_PROTEIN_TARGETING_TO_MEMBRANE, ONKEN_UVEAL_MELANOMA_UP, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_REGULATION_OF_CELLULAR_LOCALIZATION, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE, DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN, LIAO_METASTASIS, GOCC_APICOLATERAL_PLASMA_MEMBRANE

GO Biological Process (6): microtubule bundle formation (GO:0001578), chromosome segregation (GO:0007059), regulation of autophagy (GO:0010506), establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197), cell division (GO:0051301), positive regulation of protein targeting to membrane (GO:0090314)

GO Molecular Function (4): RNA binding (GO:0003723), microtubule binding (GO:0008017), protein homodimerization activity (GO:0042803), protein binding (GO:0005515)

GO Cellular Component (13): kinetochore (GO:0000776), spindle pole (GO:0000922), obsolete extracellular space (GO:0005615), cytoskeleton (GO:0005856), spindle microtubule (GO:0005876), apical plasma membrane (GO:0016324), apicolateral plasma membrane (GO:0016327), lateral plasma membrane (GO:0016328), midbody (GO:0030496), microtubule bundle (GO:0097427), cytoplasm (GO:0005737), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	6
intracellular membraneless organelle	2
spindle	2
microtubule	2
plasma membrane region	2
microtubule cytoskeleton organization	1
cell cycle process	1
autophagy	1
regulation of catabolic process	1
establishment or maintenance of apical/basal cell polarity	1
cellular process	1
protein targeting to membrane	1
positive regulation of cellular process	1
regulation of protein targeting to membrane	1
positive regulation of establishment of protein localization	1
nucleic acid binding	1
tubulin binding	1
identical protein binding	1
protein dimerization activity	1
binding	1
condensed chromosome, centromeric region	1
supramolecular complex	1
apical part of cell	1
plasma membrane	1
cytoskeleton	1
intracellular anatomical structure	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

638 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MTCL1	PPP2R5E	Q16537	572
MTCL1	GSTCD	Q8NEC7	474
MTCL1	EEFSEC	P57772	469
MTCL1	FAM13A	O94988	453
MTCL1	TRIM46	Q7Z4K8	425
MTCL1	SGF29	Q96ES7	390
MTCL1	AKAIN1	P0CW23	379
MTCL1	CORO1C	Q9ULV4	374
MTCL1	ANKRD12	Q6UB98	358
MTCL1	RBM12B	Q8IXT5	358
MTCL1	AKAP9	Q99996	349
MTCL1	CAMSAP2	Q08AD1	348
MTCL1	TUT1	Q9H6E5	339
MTCL1	NPNT	Q6UXI9	322
MTCL1	LTN1	O94822	312

IntAct

95 interactions, top by confidence:

A	B	Type	Score
PPP2R1A	STRN	psi-mi:“MI:0914”(association)	0.880
SNX6	SNX2	psi-mi:“MI:0914”(association)	0.800
ANKRD44	PPP6C	psi-mi:“MI:0914”(association)	0.790
DYNLL1	BLTP3B	psi-mi:“MI:0914”(association)	0.730
PPP2R2C	PPP2R1A	psi-mi:“MI:0914”(association)	0.730
ANKRD44	ANKRD28	psi-mi:“MI:0914”(association)	0.710
PPP2R5A	PPP2R1B	psi-mi:“MI:0914”(association)	0.670
PPP2R2B	MYO9A	psi-mi:“MI:0914”(association)	0.640
DYNLL2	BLTP3B	psi-mi:“MI:0914”(association)	0.640
CAPZB	CNOT1	psi-mi:“MI:0914”(association)	0.640
CAPZA2	CNOT1	psi-mi:“MI:0914”(association)	0.640
P4HA3	FAM171A2	psi-mi:“MI:0914”(association)	0.640
CAPZA1	CNOT1	psi-mi:“MI:0914”(association)	0.530
PPP2R5A	AXIN1	psi-mi:“MI:0914”(association)	0.530
ZNF223	CENPB	psi-mi:“MI:0914”(association)	0.530
WDR83	SH2B2	psi-mi:“MI:0914”(association)	0.530
NDEL1	OFD1	psi-mi:“MI:0914”(association)	0.530
NCK1	SH3PXD2B	psi-mi:“MI:0914”(association)	0.530

BioGRID (134): MTCL1 (Affinity Capture-RNA), MTCL1 (Affinity Capture-RNA), MTCL1 (Affinity Capture-MS), MTCL1 (Affinity Capture-Western), MARK2 (Affinity Capture-Western), MARK2 (Reconstituted Complex), MTCL1 (Reconstituted Complex), MTCL1 (Reconstituted Complex), MTCL1 (Reconstituted Complex), MTCL1 (Affinity Capture-MS), MTCL1 (Affinity Capture-MS), MTCL1 (Affinity Capture-MS), MTCL1 (Affinity Capture-MS), MTCL1 (Biochemical Activity), MTCL1 (Biochemical Activity)

ESM2 similar proteins: A0A140LIT1, A0A1B0GVG4, A0A494C0Y3, A0JNH6, A0JNN8, A1A5D9, A2ARS0, A5A769, A5PJP1, A6NC98, A7YWC8, C9JTQ0, O15049, O35764, O95502, P0C7N4, P0DPE3, P58660, Q0P5D1, Q1HCM0, Q2TAC2, Q3LUD3, Q3LUD4, Q3TMW1, Q3UMT1, Q4QRL3, Q5BLP8, Q5JTB6, Q6QNY0, Q6QZQ4, Q8BP01, Q8C7U1, Q8CHW5, Q8K262, Q8N283, Q8N6Y0, Q8TAT2, Q8TER5, Q8TF21, Q91XV7

Diamond homologs: E1U8D0, O94964, Q3UHU5, Q5TF21, Q6NZL0, Q9Y4B5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 122 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
RAF activation	5	21.8×	5e-05
Negative regulation of MAPK pathway	5	17.2×	1e-04
Loss of Nlp from mitotic centrosomes	7	14.4×	2e-05
Loss of proteins required for interphase microtubule organization from the centrosome	7	14.4×	2e-05
AURKA Activation by TPX2	7	13.8×	2e-05
COPI-independent Golgi-to-ER retrograde traffic	5	13.5×	4e-04
Regulation of PLK1 Activity at G2/M Transition	8	13.2×	2e-05
Antimicrobial mechanism of IFN-stimulated genes	5	12.8×	4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	299
Likely benign	47
Benign	6

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2431351	NM_001395333.1(MTCL1):c.1129C>T (p.Gln377Ter)	Pathogenic

SpliceAI

3716 predictions. Top by Δscore:

Variant	Effect	Δscore
18:8718412:T:TA	acceptor_gain	1.0000
18:8718417:T:TA	acceptor_gain	1.0000
18:8718419:CATAG:C	acceptor_loss	1.0000
18:8718420:A:AG	acceptor_gain	1.0000
18:8718420:ATAG:A	acceptor_gain	1.0000
18:8718421:T:G	acceptor_gain	1.0000
18:8718421:TA:T	acceptor_loss	1.0000
18:8718421:TAGGA:T	acceptor_gain	1.0000
18:8718422:A:AG	acceptor_gain	1.0000
18:8718422:AG:A	acceptor_gain	1.0000
18:8718422:AGGAT:A	acceptor_gain	1.0000
18:8718423:G:A	acceptor_gain	1.0000
18:8718423:G:GC	acceptor_gain	1.0000
18:8718423:GGA:G	acceptor_gain	1.0000
18:8718423:GGAT:G	acceptor_gain	1.0000
18:8718423:GGATG:G	acceptor_gain	1.0000
18:8718645:GAAG:G	donor_gain	1.0000
18:8718646:AAGG:A	donor_loss	1.0000
18:8718648:GGTG:G	donor_loss	1.0000
18:8718649:G:GG	donor_gain	1.0000
18:8720326:G:A	acceptor_gain	1.0000
18:8720334:GCAG:G	acceptor_loss	1.0000
18:8720335:CA:C	acceptor_loss	1.0000
18:8720336:A:AG	acceptor_gain	1.0000
18:8720337:G:GG	acceptor_gain	1.0000
18:8720337:GGTA:G	acceptor_gain	1.0000
18:8720494:GAG:G	donor_gain	1.0000
18:8720495:AGG:A	donor_loss	1.0000
18:8720496:GGT:G	donor_loss	1.0000
18:8720497:G:GC	donor_loss	1.0000

AlphaMissense

13076 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
18:8706709:T:C	L350P	1.000
18:8718560:T:C	L397P	1.000
18:8783764:G:C	A578P	1.000
18:8783795:T:C	L588P	1.000
18:8718440:T:C	L357P	0.999
18:8718548:T:C	L393P	0.999
18:8718557:G:C	R396P	0.999
18:8718568:G:C	A400P	0.999
18:8783732:T:C	L567P	0.999
18:8783744:T:C	L571P	0.999
18:8783780:G:C	R583P	0.999
18:8783945:T:C	L638P	0.999
18:8783965:G:C	A645P	0.999
18:8783975:T:C	L648P	0.999
18:8706688:T:C	L343P	0.998
18:8718518:T:C	L383P	0.998
18:8718526:G:C	A386P	0.998
18:8718542:G:C	R391P	0.998
18:8718545:T:C	I392T	0.998
18:8718556:C:A	R396S	0.998
18:8718563:G:C	R398P	0.998
18:8720341:G:C	A428P	0.998
18:8720375:T:C	L439P	0.998
18:8783738:T:C	L569P	0.998
18:8783750:T:C	L573P	0.998
18:8783810:G:C	R593P	0.998
18:8783950:T:C	F640L	0.998
18:8783952:T:A	F640L	0.998
18:8783952:T:G	F640L	0.998
18:8824727:T:C	F1392L	0.998

dbSNP variants (sampled 300 via entrez): RS1000002519 (18:8705742 C>G), RS1000029746 (18:8764633 C>A,G,T), RS1000030394 (18:8799695 G>A,T), RS1000033614 (18:8705538 C>A,G), RS1000077370 (18:8780475 G>A), RS1000129512 (18:8800231 TCA>T), RS1000140036 (18:8805322 A>C,G), RS1000235384 (18:8723006 A>G), RS1000264112 (18:8749152 A>C,G), RS1000282408 (18:8794811 C>T), RS1000285745 (18:8722407 A>G), RS1000290534 (18:8712388 C>G), RS1000340487 (18:8716386 T>C), RS1000342097 (18:8788443 T>C), RS1000432403 (18:8717605 G>A)

Disease associations

OMIM: gene MIM:615766 | disease phenotypes: MIM:164400

GenCC curated gene-disease

Disease	Classification	Inheritance
hereditary neurological disease	Strong	Autosomal recessive

Mondo (3): autosomal dominant cerebellar ataxia (MONDO:0020380), cerebellar ataxia (MONDO:0000437), hereditary neurological disease (MONDO:0100545)

Orphanet (2): Autosomal dominant cerebellar ataxia (Orphanet:99), Rare ataxia (Orphanet:102002)

HPO phenotypes

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

GWAS associations

13 associations (top):

Study	Trait	p-value
GCST002735_1	Breast cancer	7.000000e-06
GCST003073_17	Cerebral amyloid deposition (PET imaging)	4.000000e-06
GCST003073_9	Cerebral amyloid deposition (PET imaging)	3.000000e-07
GCST003485_12	Response to fenofibrate (HDL cholesterol levels)	7.000000e-07
GCST004147_29	Chronic obstructive pulmonary disease	6.000000e-09
GCST006481_22	Lung function (FEV1)	2.000000e-08
GCST006481_35	Lung function (FEV1)	1.000000e-07
GCST007429_77	Lung function (FVC)	2.000000e-09
GCST007430_3	Peak expiratory flow	1.000000e-13
GCST007431_133	Lung function (FEV1/FVC)	7.000000e-21
GCST007432_194	FEV1	1.000000e-24
GCST007692_5	Chronic obstructive pulmonary disease	1.000000e-11
GCST90007009_4	Gut microbiota relative abundance (Faecalibacterium)	5.000000e-06

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0007707	cerebral amyloid deposition measurement
EFO:0007805	HDL cholesterol change measurement
EFO:0004314	forced expiratory volume
EFO:0004312	vital capacity
EFO:0009718	peak expiratory flow
EFO:0004713	FEV/FVC ratio
EFO:0007874	gut microbiome measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D002524	Cerebellar Ataxia	C10.228.140.252.190; C10.597.350.090.500; C23.888.592.350.090.200

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs2377898	MTCL1		0.00	0

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, increases methylation, decreases expression	3
Acetaminophen	increases expression	2
Benzo(a)pyrene	decreases methylation, increases expression	2
Particulate Matter	decreases expression, increases abundance, affects expression	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
methylmercuric chloride	increases expression	1
bisphenol A	decreases expression	1
sodium arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
coumarin	decreases phosphorylation	1
jinfukang	decreases expression, affects cotreatment	1
NSC 689534	affects binding, decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Caffeine	affects phosphorylation	1
Cisplatin	decreases expression, affects cotreatment	1
Copper	affects binding, decreases expression	1
Doxorubicin	decreases expression	1
Estradiol	increases expression	1
Ivermectin	decreases expression	1
Melphalan	decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Triclosan	decreases expression	1
Cyclosporine	decreases expression, increases methylation	1
Aflatoxin B1	increases methylation	1
Antirheumatic Agents	increases expression	1
Okadaic Acid	increases expression	1
Nanotubes, Carbon	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00950196	PHASE4	COMPLETED	Amantadine for Improving Neurologic Symptoms in Ataxia-Telangiectasia
NCT04107740	PHASE4	COMPLETED	C-Trelin Orally Disintegrated(OD) Tablet 5mg in Ataxia Due to Spinocerebellar Degeneration
NCT03408080	PHASE3	ACTIVE_NOT_RECRUITING	Open Pilot Trial of BHV-4157
NCT03701399	PHASE3	ACTIVE_NOT_RECRUITING	Troriluzole in Adult Participants With Spinocerebellar Ataxia
NCT01970098	PHASE3	COMPLETED	A Confirmatory Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01970111	PHASE3	COMPLETED	An Extension Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01970124	PHASE3	COMPLETED	A Long-Term Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01970137	PHASE3	COMPLETED	A 24-week Open-label Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT02889302	PHASE3	COMPLETED	An Additional Confirmatory Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT03901638	PHASE3	TERMINATED	Tllsh2910 for Ataxia and Gut Microbiota Alteration in Patients of Multiple System Atrophy
NCT07040137	PHASE3	RECRUITING	Confirmatory Study 3 of KPS-0373 in Patients With Spinocerebellar Degeneration
NCT01350440	PHASE2	COMPLETED	Safety and Efficacy of Intravenous Immune Globulin in Treating Spinocerebellar Ataxia
NCT04301284	PHASE2	WITHDRAWN	Study of CAD-1883 for Spinocerebellar Ataxia
NCT06397274	PHASE2	NOT_YET_RECRUITING	Stemchymal® for Polyglutamine Spinocerebellar Ataxia
NCT00034242	PHASE2	COMPLETED	High-Dose Intravenous Immunoglobulin to Treat Cerebellar Degeneration
NCT00202397	PHASE2	COMPLETED	Effect of Riluzole as a Symptomatic Approach in Patients With Chronic Cerebellar Ataxia
NCT00863538	PHASE2	COMPLETED	Phase II Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01004016	PHASE2	COMPLETED	A Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT02540655	PHASE2	COMPLETED	Efficacy and Safety Study of Stemchymal® in Polyglutamine Spinocerebellar Ataxia
NCT03932669	PHASE2	COMPLETED	Effect of Nilotinib in Cerebellar Ataxia Patients
NCT05125666	PHASE2	UNKNOWN	Efficacy of Dual Task Training on Children With Ataxia After Medulloblastoma Resection
NCT00683943	PHASE1	COMPLETED	Lithium Treatment for Patients With Spinocerebellar Ataxia Type I
NCT02287064	PHASE1	UNKNOWN	An Open-label Trial of Intravenous Immune Globulin (IVIG)in Treating Spinocerebellar Ataxias
NCT05157802	PHASE1	ACTIVE_NOT_RECRUITING	Promoting Physical Activity Engagement for People With Early-stage Cerebellar Ataxia
NCT06955624	Not specified	RECRUITING	Use of Omics Methods to Classify Variations of Uncertain Significance and Improve Diagnosis of Neurogenetic Diseases
NCT02960893	PHASE2/PHASE3	COMPLETED	Trial in Adult Participants With Spinocerebellar Ataxia (SCA)
NCT00136630	Not specified	COMPLETED	Natural History, Genetic Bases and Phenotype-genotype Correlations in Autosomal Dominant Spinocerebellar Degenerations
NCT00654251	Not specified	COMPLETED	Measuring Neurological Impairment and Functional Visual Assessment In Spinocerebellar Ataxias
NCT01037777	Not specified	COMPLETED	RISCA : Prospective Study of Individuals at Risk for SCA1, SCA2, SCA3, SCA6, SCA7
NCT01793168	Not specified	RECRUITING	Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT01975909	Not specified	COMPLETED	Transcranial Magnetic Stimulation in Spino-Cerebellar Ataxia
NCT01983631	Not specified	COMPLETED	The Effect of Whole Body Vibration Training on Neuromuscular Property in Individuals With Ataxia
NCT02103075	Not specified	COMPLETED	Neuromuscular Electrical Stimulation on Median Nerve Facilitates Low Motor Cortex Excitability in Human With Spinocerebellar Ataxia
NCT02440763	Not specified	RECRUITING	The EUROSCA Natural History Study
NCT02488031	Not specified	COMPLETED	Functional and Structural Imaging and Motor Control in Spinocerebellar Ataxia
NCT02741440	Not specified	RECRUITING	Natural History of Spinocerebellar Ataxia Type 7 (SCA7)
NCT02867969	Not specified	UNKNOWN	Slowing Down Disease Progression in Premanifest SCA: a Piloting Interventional Exergame Trial
NCT02874911	Not specified	COMPLETED	Coordination Training With Complete Body Video Games in Children and Adults With Degenerative Ataxias
NCT03120013	Not specified	COMPLETED	Rehabilitative Trial With Cerebello-Spinal tDCS in Neurodegenerative Ataxia
NCT03336008	Not specified	RECRUITING	Hong Kong Spinocerebellar Ataxias Registry