THADA

Summary

THADA (THADA armadillo repeat containing, HGNC:19217) is a protein-coding gene on chromosome 2p21, encoding tRNA (32-2’-O)-methyltransferase regulator THADA (Q6YHU6). Together with methyltransferase FTSJ1, methylates the 2’-O-ribose of nucleotides at position 32 of the anticodon loop of substrate tRNAs.

This gene is the target of 2p21 choromosomal aberrations in benign thyroid adenomas. Single nucleotide polymorphisms (SNPs) in this gene may be associated with type 2 diabetes and polycystic ovary syndrome. The encoded protein is likely involved in the death receptor pathway and apoptosis.

Source: NCBI Gene 63892 — RefSeq curated summary.

At a glance

• GWAS associations: 111
• Clinical variants (ClinVar): 436 total
• MANE Select transcript: NM_022065

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19217
Approved symbol	THADA
Name	THADA armadillo repeat containing
Location	2p21
Locus type	gene with protein product
Status	Approved
Aliases	FLJ21877, KIAA1767, GITA, ARMC13, Trm732
Ensembl gene	ENSG00000115970
Ensembl biotype	protein_coding
OMIM	611800
Entrez	63892

Gene structure

Transcript identifiers

Ensembl transcripts: 36 — 23 protein_coding, 8 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay, 1 retained_intron

ENST00000398653, ENST00000402360, ENST00000402796, ENST00000403856, ENST00000404790, ENST00000405006, ENST00000405975, ENST00000407351, ENST00000408045, ENST00000436947, ENST00000462185, ENST00000467668, ENST00000469323, ENST00000473004, ENST00000474159, ENST00000485018, ENST00000485353, ENST00000486735, ENST00000497770, ENST00000855630, ENST00000855631, ENST00000855632, ENST00000855633, ENST00000855634, ENST00000855635, ENST00000855636, ENST00000855637, ENST00000855638, ENST00000855639, ENST00000915746, ENST00000944892, ENST00000944893, ENST00000944894, ENST00000944895, ENST00000944896, ENST00000944897

RefSeq mRNA: 7 — MANE Select: NM_022065 NM_001083953, NM_001271643, NM_001271644, NM_001345923, NM_001345924, NM_001345925, NM_022065

CCDS: CCDS46268, CCDS62901, CCDS62902

Canonical transcript exons

ENST00000405975 — 38 exons

Exon	Start	End
ENSE00001534232	43595931	43596038
ENSE00001549683	43230851	43231343
ENSE00003459890	43551789	43551925
ENSE00003464049	43232713	43232882
ENSE00003465855	43527879	43527988
ENSE00003467788	43586702	43586734
ENSE00003479288	43428100	43428231
ENSE00003482778	43291696	43291768
ENSE00003495137	43344122	43344237
ENSE00003509329	43508648	43508780
ENSE00003523943	43566698	43566821
ENSE00003526048	43279765	43279896
ENSE00003529481	43397971	43398139
ENSE00003534400	43292104	43292222
ENSE00003534437	43430213	43430302
ENSE00003539234	43590824	43590954
ENSE00003549052	43581741	43581928
ENSE00003550452	43578513	43578607
ENSE00003555223	43505622	43505735
ENSE00003557220	43549210	43549368
ENSE00003561122	43320446	43320540
ENSE00003571279	43560234	43560385
ENSE00003580516	43286908	43287061
ENSE00003588378	43556345	43556555
ENSE00003590105	43586401	43586449
ENSE00003592591	43292834	43293213
ENSE00003601144	43586854	43587002
ENSE00003602671	43577022	43577242
ENSE00003617160	43552204	43552339
ENSE00003627376	43572814	43572992
ENSE00003638489	43485234	43485325
ENSE00003645202	43570388	43570510
ENSE00003645494	43541159	43541316
ENSE00003648495	43591952	43592046
ENSE00003655012	43592317	43592416
ENSE00003658609	43498833	43498955
ENSE00003660316	43571707	43571862
ENSE00003673154	43574336	43575027

Expression profiles

Bgee: expression breadth ubiquitous, 276 present calls, max score 92.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.5409 / max 155.1186, expressed in 1807 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
28097	17.9644	1801
28096	1.0657	668
28084	0.1882	94
28086	0.1419	73
28087	0.0711	27
28088	0.0691	15
28093	0.0292	9
28089	0.0114	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	92.93	gold quality
right uterine tube	UBERON:0001302	92.50	gold quality
right lobe of thyroid gland	UBERON:0001119	91.97	gold quality
left lobe of thyroid gland	UBERON:0001120	91.38	gold quality
tendon	UBERON:0000043	91.36	gold quality
thyroid gland	UBERON:0002046	90.81	gold quality
tendon of biceps brachii	UBERON:0008188	90.69	gold quality
sural nerve	UBERON:0015488	88.77	gold quality
lower esophagus mucosa	UBERON:0035834	88.71	gold quality
skin of leg	UBERON:0001511	88.59	gold quality
adenohypophysis	UBERON:0002196	88.50	gold quality
right lobe of liver	UBERON:0001114	88.44	gold quality
skin of abdomen	UBERON:0001416	88.44	gold quality
pituitary gland	UBERON:0000007	88.38	gold quality
prostate gland	UBERON:0002367	88.22	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.20	gold quality
spleen	UBERON:0002106	88.15	gold quality
body of uterus	UBERON:0009853	88.04	gold quality
ventricular zone	UBERON:0003053	87.99	gold quality
endocervix	UBERON:0000458	87.98	gold quality
tibial nerve	UBERON:0001323	87.85	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.45	gold quality
tonsil	UBERON:0002372	87.45	gold quality
right ovary	UBERON:0002118	87.32	gold quality
left ovary	UBERON:0002119	87.26	gold quality
adrenal tissue	UBERON:0018303	87.12	gold quality
zone of skin	UBERON:0000014	87.01	gold quality
minor salivary gland	UBERON:0001830	86.83	gold quality
bronchial epithelial cell	CL:0002328	86.74	gold quality
granulocyte	CL:0000094	86.71	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-124858	no	292.56
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting THADA, 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-4282	99.99	75.36	6408
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-3074-5P	98.82	66.56	1414
HSA-MIR-7847-3P	96.63	64.58	952
HSA-MIR-12115	94.19	66.37	738

Literature-anchored findings (GeneRIF, showing 18)

• identification of the target gene of 2p21 aberrations in thyroid adenomas tentatively referred to as thyroid adenoma-associated gene (THADA); gene spans roughly 365 kbp; based on preliminary results, it encodes a death receptor-interacting protein [THADA] (PMID:12955091)
• intronic sequence of PPAR(gamma) is fused to exon 28 of THADA in thyroid tumors of follicular origin including carcinomas as well as adenomas (PMID:17123335)
• At least two of the PCOS susceptibility loci identified in the Chinese PCOS GWAS (DENND1A and THADA) are also associated with PCOS in European derived populations. (PMID:22180642)
• DNA methylation of genes in retinol metabolism and calcium signaling pathways (P < 3 x 10-6) and with known functions in muscle and T2D including MEF2A, RUNX1, NDUFC2, and THADA decreased after exercise (PMID:23028138)
• THADA and DENND1A, carry risk alleles that are associated with endocrine and metabolic disturbances in PCOS patients of Han Chinese descent. (PMID:23208300)
• Data indicate associations of SNPs in eight loci CXCR4, HHEX, FOXA2, NGN3, TCF7L2, FLJ39370 (C4orf32), LOC646279 (RPL21P7) and THADA with body mass index (BMI) and weight. (PMID:23349771)
• In addition, eight genes classified as ‘second tier’ hits in the original study (PAX7, THADA, COL8A1/FILIP1L, DCAF4L2, GADD45G, NTN1, RBFOX3 and FOXE1) showed evidence of linkage and association in this replication sample. (PMID:23512105)
• Our results showed that rs1465618 in THADA may be a shared susceptibility variant for PCa in multiple populations. (PMID:24685913)
• association of the THADA, FOXP4, GPRC6A/RFX6 and 8q24 genes with prostate cancer in Asian populations. (PMID:26537068)
• THADA fusion is a mechanism of IGF2BP3 activation and IGF1R signaling in thyroid cancer. (PMID:28193878)
• this identifies THADA as a regulator of the balance between energy consumption and energy storage, which was selected during human evolution. (PMID:28399403)
• Genetic variants of PCOS (rs13405728 in LHCGR gene; rs13429458 in THADA gene and rs2479106 in DENND1A gene) may not be involved in the development of preeclampsia in Han Chinese women. (PMID:29727258)
• THADA_rs13429458 Minor Allele is associated with Polycystic Ovary Syndrome in Asian, but Not in Caucasian Women. (PMID:31487746)
• Of the 15 variants, 3 variants (rs13405728 in LHCGR; rs13429458 in THADA and rs2209972 IDE genes) were found to be associated with PCOS. The association was successfully replicated in an independent cohort. Insilico analysis categorized two variants (rs13429458-THADA and rs2209972-IDE genes) as deleterious. (PMID:32416252)
• Clinicopathologic Characteristics of Thyroid Nodules Positive for the THADA-IGF2BP3 Fusion on Preoperative Molecular Analysis. (PMID:33487086)
• Replication study of THADA rs13429458 variant with PCOS susceptibility and its related traits in Indian women. (PMID:33779462)
• THADA, SDHAF4, and MACF1 Gene Polymorphisms and Placental Expression in Women with Gestational Diabetes. (PMID:36672824)
• Negative regulation of thyroid adenoma-associated protein (THADA) in the cardiac glycoside-induced anti-cancer effect. (PMID:38561668)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	thada	ENSDARG00000053082
mus_musculus	Thada	ENSMUSG00000024251
rattus_norvegicus	Thada	ENSRNOG00000025899
drosophila_melanogaster	THADA	FBGN0031077
caenorhabditis_elegans	Y92H12A.5	WBGENE00022361

Protein

Protein identifiers

tRNA (32-2’-O)-methyltransferase regulator THADA — Q6YHU6 (reviewed: Q6YHU6)

Alternative names: Gene inducing thyroid adenomas protein, Thyroid adenoma-associated protein

All UniProt accessions (6): B5MC89, B6ZDE5, Q6YHU6, F5H3M9, H0Y3V5, H7BYZ4

UniProt curated annotations — full annotation on UniProt →

Function. Together with methyltransferase FTSJ1, methylates the 2’-O-ribose of nucleotides at position 32 of the anticodon loop of substrate tRNAs.

Tissue specificity. Expressed in pancreas, adrenal medulla, thyroid, adrenal cortex, testis, thymus, small intestine and stomach.

Disease relevance. Chromosomal aberrations involving THADA have been observed in benign thyroid adenomas. Translocation t(2;3)(p21;p25) and translocation t(2;7)(p21;p15); the sequences derived from chromosomes 3p25 and 7p15 do not appear to include a coding region and the fusion events probably result in truncated THADA proteins.

Similarity. Belongs to the THADA family.

Isoforms (6)

UniProt ID	Names	Canonical?
Q6YHU6-1	1	yes
Q6YHU6-2	2, GITA-A2
Q6YHU6-3	3
Q6YHU6-4	4
Q6YHU6-5	5
Q6YHU6-6	6

RefSeq proteins (7): NP_001077422, NP_001258572, NP_001258573, NP_001332852, NP_001332853, NP_001332854, NP_071348* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR016024	ARM-type_fold	Homologous_superfamily
IPR019442	THADA/TRM732_DUF2428	Domain
IPR051954	tRNA_methyltransferase_THADA	Family
IPR056842	THADA-like_TPR_C	Domain
IPR056843	THADA-like_TPR	Domain

Pfam: PF10350, PF25150, PF25151

UniProt features (24 total): splice variant 8, sequence variant 7, modified residue 3, sequence conflict 3, chain 1, coiled-coil region 1, helix 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
5T6Y	X-RAY DIFFRACTION	1.76
8Y2O	ELECTRON MICROSCOPY	2.66

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6YHU6-F1	80.13	0.26

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 (3): 1015, 1024, 1161

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-6782315	tRNA modification in the nucleus and cytosol
R-HSA-72306	tRNA processing
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 177 (showing top): ATF_B, GGGACCA_MIR133A_MIR133B, GOBP_TRNA_METABOLIC_PROCESS, GOBP_RNA_METHYLATION, GOBP_LIPID_HOMEOSTASIS, GOBP_RNA_MODIFICATION, TGTGTGA_MIR377, GOBP_TRNA_METHYLATION, GARY_CD5_TARGETS_DN, CREB_Q2_01, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, GOBP_ENDOPLASMIC_RETICULUM_CALCIUM_ION_HOMEOSTASIS, ATF4_Q2, GOBP_MONOATOMIC_ION_HOMEOSTASIS, ATGTCAC_MIR489

GO Biological Process (6): tRNA nucleoside ribose methylation (GO:0002128), tRNA methylation (GO:0030488), negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471), lipid homeostasis (GO:0055088), adaptive thermogenesis (GO:1990845), tRNA processing (GO:0008033)

GO Molecular Function (2): enzyme regulator activity (GO:0030234), protein binding (GO:0005515)

GO Cellular Component (2): cytoplasmic side of endoplasmic reticulum membrane (GO:0098554), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
tRNA processing	1
Metabolism of RNA	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
tRNA methylation	1
RNA methylation	1
tRNA modification	1
endoplasmic reticulum calcium ion homeostasis	1
chemical homeostasis	1
temperature homeostasis	1
RNA processing	1
tRNA metabolic process	1
catalytic activity	1
molecular function regulator activity	1
binding	1
endoplasmic reticulum membrane	1
cytoplasmic side of membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1300 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
THADA	DENND1A	Q8TEH3	640
THADA	WDR6	Q9NNW5	536
THADA	FTSJ1	Q9UET6	491
THADA	CARF	Q8N187	457
THADA	JAZF1	Q86VZ6	449
THADA	FGF20	Q9NP95	440
THADA	FBN3	Q75N90	398
THADA	AOPEP	Q8N6M6	398
THADA	CDC123	O75794	393
THADA	HHEX	Q03014	379
THADA	TSPAN8	P19075	375
THADA	CDKAL1	Q5VV42	374
THADA	LHCGR	P22888	372
THADA	PLEKHH2	Q8IVE3	368
THADA	CAPN10	Q9HC96	360

IntAct

145 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
SCN2B	EXOC5	psi-mi:“MI:0914”(association)	0.640
CCKBR	PRKAG1	psi-mi:“MI:0914”(association)	0.640
ILVBL	COG7	psi-mi:“MI:0914”(association)	0.640
THADA	USHBP1	psi-mi:“MI:0915”(physical association)	0.560
USHBP1	THADA	psi-mi:“MI:0915”(physical association)	0.560
THADA	ATN1	psi-mi:“MI:0915”(physical association)	0.560
KLK6	THADA	psi-mi:“MI:0915”(physical association)	0.560
OPTN	THADA	psi-mi:“MI:0915”(physical association)	0.560
THADA		psi-mi:“MI:0915”(physical association)	0.550
APLNR	METTL15	psi-mi:“MI:0914”(association)	0.530
VASN	AP3B1	psi-mi:“MI:0914”(association)	0.530
CD226	MEN1	psi-mi:“MI:0914”(association)	0.530
CA14	EXOC5	psi-mi:“MI:0914”(association)	0.530
ILVBL	EIF2B5	psi-mi:“MI:0914”(association)	0.530
FAM174A	BLTP3B	psi-mi:“MI:0914”(association)	0.530
CD70	METTL15	psi-mi:“MI:0914”(association)	0.530
ILVBL	SLC33A1	psi-mi:“MI:0914”(association)	0.530
APLNR	SLC33A1	psi-mi:“MI:0914”(association)	0.530
CD40	EXOC5	psi-mi:“MI:0914”(association)	0.530
GPR17	IPO8	psi-mi:“MI:0914”(association)	0.530

BioGRID (153): USHBP1 (Two-hybrid), THADA (Affinity Capture-MS), THADA (Affinity Capture-MS), THADA (Affinity Capture-MS), THADA (Affinity Capture-MS), THADA (Affinity Capture-MS), THADA (Affinity Capture-MS), THADA (Affinity Capture-MS), THADA (Affinity Capture-MS), THADA (Affinity Capture-MS), THADA (Affinity Capture-MS), THADA (Affinity Capture-MS), THADA (Affinity Capture-MS), THADA (Affinity Capture-MS), THADA (Affinity Capture-MS)

ESM2 similar proteins: A1L3L1, A2RT67, A3KPW7, A4IIA7, A8C750, A8C752, D2HNY3, E1BGQ2, E1C3P4, Q08CL8, Q08DZ8, Q0IHB3, Q149N8, Q1RMU2, Q1RMZ1, Q3MJ13, Q3T1H6, Q5F3F2, Q5RED8, Q5VVJ2, Q5ZJ87, Q66J91, Q69Z66, Q6AYF5, Q6DE97, Q6GR37, Q6P1E7, Q6PNC0, Q6YHU6, Q7TPQ3, Q8BKW4, Q8BXK4, Q8IWR0, Q8IYF3, Q8IZE3, Q8K2I9, Q8NA31, Q8NEN0, Q8NFZ0, Q96EW2

Diamond homologs: A8C750, A8C752, A8C754, A8C756, Q6YHU6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 164 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
Transport of vitamins, nucleosides, and related molecules	5	12.9×	4e-03
Peptide ligand-binding receptors	10	7.1×	7e-04
Class A/1 (Rhodopsin-like receptors)	9	6.4×	2e-03
GPCR ligand binding	9	5.5×	4e-03
G alpha (q) signalling events	9	4.9×	6e-03
G alpha (i) signalling events	11	4.1×	6e-03

GO biological processes:

GO term	Partners	Fold	FDR
T cell costimulation	7	18.7×	3e-05
adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway	9	14.1×	9e-06
phospholipase C-activating G protein-coupled receptor signaling pathway	9	8.5×	4e-04
positive regulation of cytosolic calcium ion concentration	9	7.5×	8e-04
cell surface receptor signaling pathway	11	5.0×	2e-03
G protein-coupled receptor signaling pathway	19	4.9×	9e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	334
Likely benign	40
Benign	20

Top pathogenic / likely-pathogenic (0)

SpliceAI

7035 predictions. Top by Δscore:

Variant	Effect	Δscore
2:43231339:TCCAC:T	acceptor_gain	1.0000
2:43231340:CCAC:C	acceptor_gain	1.0000
2:43231340:CCACC:C	acceptor_gain	1.0000
2:43231341:CAC:C	acceptor_gain	1.0000
2:43231341:CACC:C	acceptor_gain	1.0000
2:43231342:AC:A	acceptor_gain	1.0000
2:43231343:CC:C	acceptor_gain	1.0000
2:43231344:C:CC	acceptor_gain	1.0000
2:43231350:C:CT	acceptor_gain	1.0000
2:43231351:A:T	acceptor_gain	1.0000
2:43231353:A:AC	acceptor_gain	1.0000
2:43231353:A:C	acceptor_gain	1.0000
2:43232709:TCAC:T	donor_loss	1.0000
2:43232711:A:C	donor_loss	1.0000
2:43232712:C:CT	donor_loss	1.0000
2:43232726:T:A	donor_gain	1.0000
2:43232878:AAACT:A	acceptor_gain	1.0000
2:43232879:AACT:A	acceptor_gain	1.0000
2:43232880:ACT:A	acceptor_gain	1.0000
2:43232881:CT:C	acceptor_gain	1.0000
2:43232881:CTC:C	acceptor_gain	1.0000
2:43232882:TC:T	acceptor_loss	1.0000
2:43232882:TCT:T	acceptor_gain	1.0000
2:43232883:C:CC	acceptor_gain	1.0000
2:43232883:C:G	acceptor_gain	1.0000
2:43232884:T:A	acceptor_loss	1.0000
2:43291690:CCTTA:C	donor_loss	1.0000
2:43291691:CTTA:C	donor_loss	1.0000
2:43291692:TTA:T	donor_loss	1.0000
2:43291693:TA:T	donor_loss	1.0000

AlphaMissense

12868 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:43541263:A:G	W1054R	1.000
2:43541263:A:T	W1054R	1.000
2:43508672:A:C	S1161R	0.999
2:43508672:A:T	S1161R	0.999
2:43508674:T:G	S1161R	0.999
2:43508678:C:A	R1159S	0.999
2:43508678:C:G	R1159S	0.999
2:43508679:C:A	R1159M	0.999
2:43508679:C:G	R1159T	0.999
2:43527940:G:C	H1105D	0.999
2:43541255:A:C	S1056R	0.999
2:43541255:A:T	S1056R	0.999
2:43541257:T:G	S1056R	0.999
2:43541261:C:A	W1054C	0.999
2:43541261:C:G	W1054C	0.999
2:43508667:C:T	G1163E	0.998
2:43527926:A:C	F1109L	0.998
2:43527926:A:T	F1109L	0.998
2:43527928:A:G	F1109L	0.998
2:43527938:G:C	H1105Q	0.998
2:43527938:G:T	H1105Q	0.998
2:43527954:A:G	L1100P	0.998
2:43541264:A:C	C1053W	0.998
2:43541274:A:G	L1050P	0.998
2:43551839:A:T	V966D	0.998
2:43574489:A:G	W526R	0.998
2:43574489:A:T	W526R	0.998
2:43498838:A:G	W1247R	0.997
2:43498838:A:T	W1247R	0.997
2:43508668:C:G	G1163R	0.997

dbSNP variants (sampled 300 via entrez): RS1000001782 (2:43283912 C>T), RS1000019946 (2:43427738 C>T), RS1000023158 (2:43463429 T>A,C), RS1000027260 (2:43499501 C>T), RS1000035644 (2:43409946 G>A), RS1000038354 (2:43288810 C>T), RS1000060435 (2:43586506 T>A,C), RS1000060528 (2:43435186 G>A), RS1000064077 (2:43534997 G>A), RS1000073128 (2:43540094 T>C), RS1000081175 (2:43328324 G>C), RS1000090719 (2:43317979 A>G), RS1000094291 (2:43363133 A>G), RS1000095098 (2:43243873 C>T), RS1000096132 (2:43399490 A>C)

Disease associations

OMIM: gene MIM:611800 | disease phenotypes: MIM:156000

GenCC curated gene-disease

Mondo (1): Meniere disease (MONDO:0007972)

Orphanet (1): NON RARE IN EUROPE: Menière disease (Orphanet:45360)

HPO phenotypes

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

GWAS associations

111 associations (top):

Study	Trait	p-value
GCST000167_4	Type 2 diabetes	1.000000e-09
GCST000488_7	Prostate cancer	2.000000e-08
GCST000519_13	Hair morphology	1.000000e-07
GCST000547_1	Orofacial clefts	9.000000e-08
GCST000879_11	Crohn’s disease	2.000000e-14
GCST000914_1	Polycystic ovary syndrome	2.000000e-23
GCST000914_5	Polycystic ovary syndrome	3.000000e-23
GCST001337_8	Platelet count	1.000000e-10
GCST001341_2	Multiple sclerosis	3.000000e-08
GCST001628_27	Orofacial clefts	1.000000e-08
GCST001651_38	Response to amphetamines	6.000000e-06
GCST002058_18	DNA methylation (variation)	8.000000e-07
GCST002616_16	Mitochondrial DNA levels	4.000000e-06
GCST002726_33	Glucose homeostasis traits	5.000000e-07
GCST003144_1	Polycystic ovary syndrome	3.000000e-10
GCST003372_42	Glomerular filtration rate (creatinine)	7.000000e-07
GCST003797_1	Diabetes in response to antihypertensive drug treatment (treatment strategy interaction)	5.000000e-08
GCST003797_2	Diabetes in response to antihypertensive drug treatment (treatment strategy interaction)	2.000000e-07
GCST003983_40	Male-pattern baldness	2.000000e-08
GCST004131_59	Inflammatory bowel disease	6.000000e-09
GCST004132_60	Crohn’s disease	4.000000e-11
GCST004602_81	Mean corpuscular volume	2.000000e-18
GCST004607_215	Plateletcrit	6.000000e-32
GCST004608_53	Granulocyte percentage of myeloid white cells	1.000000e-10
GCST004613_89	Sum neutrophil eosinophil counts	5.000000e-11
GCST004614_125	Granulocyte count	3.000000e-11
GCST004620_129	Sum basophil neutrophil counts	2.000000e-11
GCST004626_13	Myeloid white cell count	3.000000e-10
GCST004628_144	Immature fraction of reticulocytes	6.000000e-09
GCST004629_21	Neutrophil count	2.000000e-11

EFO canonical traits (45, from GWAS)

EFO ID	Trait name
EFO:0005038	hair morphology
EFO:0003959	cleft lip
EFO:0004309	platelet count
EFO:0022599	DNA methylation
EFO:0006312	mitochondrial DNA measurement
EFO:0004471	insulin sensitivity measurement
EFO:0005405	response to antihypertensive drug
EFO:0007766	response to beta blocker
EFO:0007767	response to calcium channel blocker
EFO:0007985	platelet crit
EFO:0007997	granulocyte percentage of myeloid white cells
EFO:0004833	neutrophil count
EFO:0004842	eosinophil count
EFO:0007987	granulocyte count
EFO:0005090	basophil count
EFO:0007986	reticulocyte count
EFO:0004527	mean corpuscular hemoglobin
EFO:0004695	intraocular pressure measurement
EFO:0009272	Epstein Barr viral capsid antigen seropositivity
EFO:0009270	heel bone mineral density
EFO:0004530	triglyceride measurement
EFO:0006335	systolic blood pressure
EFO:0009706	latent autoimmune diabetes in adults
EFO:0009924	Drugs used in diabetes use measurement
EFO:0009929	Beta blocking agent use measurement
EFO:0009931	Agents acting on the renin-angiotensin system use measurement
EFO:0006336	diastolic blood pressure
EFO:0004615	apolipoprotein B measurement
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0004468	glucose measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D008575	Meniere Disease	C09.218.568.217.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression	5
bisphenol A	affects methylation, affects cotreatment, decreases methylation, decreases expression	2
Cisplatin	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	decreases expression, increases methylation	2
Valproic Acid	decreases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
aristolochic acid I	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	decreases expression	1
sodium arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
mercuric bromide	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
bisphenol S	affects cotreatment, decreases methylation	1
jinfukang	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Vorinostat	decreases expression	1
Acetaminophen	increases expression	1
Cadmium	increases expression, increases abundance	1
Ethyl Methanesulfonate	decreases expression	1
Formaldehyde	decreases expression	1
Ribonucleotides	affects binding	1
Vincristine	increases expression	1
Vitamin E	increases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	increases methylation	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_E2LS	HAP1 THADA (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01574313	PHASE4	COMPLETED	Effect of Stellate Ganglion Block on Meniere’s Disease
NCT02529475	PHASE4	TERMINATED	Evaluation of Inner Ear and Brain Structures With Contrast-enhanced MRI in Healthy Subjects (HYDROPS)
NCT04815187	PHASE4	ACTIVE_NOT_RECRUITING	Repurposed Use of Allergic Rhinitis and Allergic Asthma Drug to Reduce Vertigo and Hearing Loss in Meniere’s Disease
NCT03664674	PHASE3	COMPLETED	Phase 3 Study of OTO-104 in Subjects With Unilateral Meniere’s Disease
NCT04677972	PHASE3	COMPLETED	SPI-1005 for the Treatment of Meniere’s Disease
NCT05851508	PHASE3	RECRUITING	The Effecttiveness of Intratympanic Methylprednisolon Injections Compared to Placebo in the Treatment of Vertigo Attacks in Meniere’s Disease
NCT05420350	PHASE2	UNKNOWN	Lamotrigine and Bupropion for Meniere’s Disease
NCT06544434	PHASE2	RECRUITING	Laser Acupuncture for Meniere Disease
NCT04674735	PHASE1	WITHDRAWN	Safety of APSLXR in Patients Presenting Vertigo of Vestibular Origin or Meniere’s Disease
NCT04218123	PHASE2/PHASE3	COMPLETED	Assessing the Efficacy of a Serotonin and Norepinephrine Reuptake Inhibitor for Improving Meniere’s Disease Outcomes
NCT04766853	PHASE1/PHASE2	COMPLETED	Verification of the Efficacy/safety of the Intratympanic Drug Delivery for Hearing Loss
NCT04794842	EARLY_PHASE1	UNKNOWN	Comparing Topical Tetracaine Drops to Topical Focal Phenol for Local Anesthesia During Intratympanic Steroid Injection
NCT00599560	Not specified	COMPLETED	Vasopressin and V2 Receptor in Meniere’s Disease
NCT02371798	Not specified	WITHDRAWN	Unilateral Meniere Disease: Can Double Dose Gadolinium and Delayed Imaging Make the Diagnosis?
NCT03520322	Not specified	TERMINATED	A Study of a Mastoid Device in Subjects With Ménière’s Disease
NCT03795675	Not specified	ACTIVE_NOT_RECRUITING	CI Following VS Removal or Labyrinthectomy
NCT04370366	Not specified	RECRUITING	Imaging of Endolymphatic Hydrops at 7T MRI
NCT04569175	Not specified	COMPLETED	Non Enhanced Labyrinth Imaging for the Detection of Endolymphatic Hydrops in Meniere’s Disease NELI Study
NCT04686695	Not specified	COMPLETED	Transcutaneous Auricular Vagus Nerve Stimulation Treatment on Meniere Disease
NCT04835688	Not specified	UNKNOWN	Ventilation Tube Insertion for Unilateral Menière’s Disease
NCT04902963	Not specified	COMPLETED	What is the Tympanic Membrane Healing Time After Insertion of a Gelfoam PE Tube?
NCT04935970	Not specified	UNKNOWN	Metabolic Disorders and Vertigo
NCT05322538	Not specified	NOT_YET_RECRUITING	Menier’s Disease - Bone Density Study
NCT05328895	Not specified	COMPLETED	Transcutaneous Auricular Vagus Nerve Stimulation for Meniere Disease
NCT05424302	Not specified	RECRUITING	Effect of Peripheral Vestibular Disease Location on Outcomes Following Home-based Virtual Reality Vestibular Therapy
NCT05582148	Not specified	UNKNOWN	Meniere Disease and Hearing Aids
NCT05844657	Not specified	COMPLETED	Comprehensive Evaluation in Patients With Meniere’s Disease
NCT05960786	Not specified	COMPLETED	Treating the Symptoms of Vertigo in a Real-world Setting Using the OtoBand
NCT06278129	Not specified	UNKNOWN	Evaluation of the Diagnostic and Prognostic Efficacy of MRI in Acute Sensorineural Hearing Loss and Ménière’s Disease
NCT06544590	Not specified	COMPLETED	Transcutaneous Auricular Vagus Nerve Stimulation for Meniere Disease
NCT07272473	Not specified	RECRUITING	Effects of Cervical Mobilization on Dizziness, Balance, and Joint Position Sense in Patients With Meniere’s Disease