TANC1

Summary

TANC1 (tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1, HGNC:29364) is a protein-coding gene on chromosome 2q24.2, encoding Protein TANC1 (Q9C0D5). May be a scaffold component in the postsynaptic density.

Predicted to be involved in regulation of postsynapse organization. Predicted to act upstream of or within dendritic spine maintenance; myoblast fusion; and visual learning. Predicted to be located in several cellular components, including axon terminus; neuronal cell body; and postsynaptic density. Predicted to be active in glutamatergic synapse and postsynaptic density, intracellular component.

Source: NCBI Gene 85461 — RefSeq curated summary.

At a glance

• GWAS associations: 11
• Clinical variants (ClinVar): 305 total
• MANE Select transcript: NM_033394

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29364
Approved symbol	TANC1
Name	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1
Location	2q24.2
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1728, ROLSB
Ensembl gene	ENSG00000115183
Ensembl biotype	protein_coding
OMIM	611397
Entrez	85461

Gene structure

Transcript identifiers

Ensembl transcripts: 52 — 48 protein_coding, 4 retained_intron

ENST00000263635, ENST00000464096, ENST00000465963, ENST00000470074, ENST00000496406, ENST00000851028, ENST00000851030, ENST00000851031, ENST00000851032, ENST00000851034, ENST00000851035, ENST00000853141, ENST00000853142, ENST00000853143, ENST00000853144, ENST00000853145, ENST00000853146, ENST00000853147, ENST00000853148, ENST00000853149, ENST00000853150, ENST00000853151, ENST00000853152, ENST00000853153, ENST00000939551, ENST00000939552, ENST00000939553, ENST00000939554, ENST00000939555, ENST00000939556, ENST00000939557, ENST00000950882, ENST00000950883, ENST00000950884, ENST00000950885, ENST00000950886, ENST00000950887, ENST00000950888, ENST00000950889, ENST00000950890, ENST00000950891, ENST00000950892, ENST00000950893, ENST00000950894, ENST00000950895, ENST00000950896, ENST00000950897, ENST00000950898, ENST00000950899, ENST00000950900, ENST00000950901, ENST00000950902

RefSeq mRNA: 6 — MANE Select: NM_033394 NM_001145909, NM_001350062, NM_001350063, NM_001350064, NM_001350065, NM_033394

CCDS: CCDS42766

Canonical transcript exons

ENST00000263635 — 27 exons

Exon	Start	End
ENSE00004283439	159097637	159097834
ENSE00004283440	159150370	159150556
ENSE00004283441	158968640	158968782
ENSE00004283442	159136194	159136298
ENSE00004283443	159194257	159194493
ENSE00004283444	159001080	159001189
ENSE00004283445	159186902	159187024
ENSE00004283446	159163283	159163546
ENSE00004283447	159219238	159219361
ENSE00004283449	159170524	159170805
ENSE00004283450	159065896	159065971
ENSE00004283451	159219692	159219867
ENSE00004283452	159225688	159225779
ENSE00004283453	159227819	159227965
ENSE00004283454	159176352	159176518
ENSE00004283455	159174953	159175184
ENSE00004283458	159172121	159172272
ENSE00004283459	159178556	159179163
ENSE00004283460	159224232	159224364
ENSE00004283461	159198975	159199053
ENSE00004283463	159217497	159217630
ENSE00004283464	159185791	159185899
ENSE00004283465	159196608	159196793
ENSE00004283473	159149142	159149272
ENSE00004283483	159228796	159228896
ENSE00004283485	159169250	159169372
ENSE00004283494	159229578	159232659

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 98.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.3836 / max 337.5611, expressed in 1582 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter ID	TPM avg	Samples expressed
23228	20.3906	1575
23229	0.6366	368
23249	0.0821	23
23248	0.0605	23
23247	0.0546	15
23243	0.0507	16
23245	0.0398	12
23256	0.0373	10
23246	0.0157	7
23250	0.0094	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper arm skin	UBERON:0004263	98.99	gold quality
cardiac muscle of right atrium	UBERON:0003379	98.88	gold quality
left ventricle myocardium	UBERON:0006566	98.78	gold quality
tibia	UBERON:0000979	98.75	gold quality
myocardium	UBERON:0002349	98.18	gold quality
upper leg skin	UBERON:0004262	98.12	gold quality
visceral pleura	UBERON:0002401	97.96	gold quality
skin of hip	UBERON:0001554	97.75	gold quality
heart right ventricle	UBERON:0002080	97.70	gold quality
germinal epithelium of ovary	UBERON:0001304	97.62	gold quality
gingival epithelium	UBERON:0001949	96.96	gold quality
lateral nuclear group of thalamus	UBERON:0002736	96.81	gold quality
esophagus squamous epithelium	UBERON:0006920	96.81	gold quality
lower lobe of lung	UBERON:0008949	96.56	gold quality
parietal pleura	UBERON:0002400	96.43	gold quality
penis	UBERON:0000989	96.18	gold quality
gingiva	UBERON:0001828	95.97	gold quality
palpebral conjunctiva	UBERON:0001812	95.96	gold quality
epithelial cell of pancreas	CL:0000083	95.67	gold quality
oral cavity	UBERON:0000167	95.42	gold quality
endothelial cell	CL:0000115	95.30	gold quality
mucosa of paranasal sinus	UBERON:0005030	95.08	gold quality
vena cava	UBERON:0004087	94.48	gold quality
mammalian vulva	UBERON:0000997	94.31	gold quality
eye	UBERON:0000970	94.26	gold quality
saphenous vein	UBERON:0007318	94.22	gold quality
sural nerve	UBERON:0015488	93.98	gold quality
epithelium of mammary gland	UBERON:0003244	93.50	gold quality
mammary duct	UBERON:0001765	93.46	gold quality
zone of skin	UBERON:0000014	93.39	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	13.41
E-MTAB-6678	yes	12.86
E-MTAB-9801	yes	6.10

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

220 targeting TANC1, 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-3924	100.00	72.09	2394
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753

Literature-anchored findings (GeneRIF, showing 3)

• Discusses cloning and expression of Rat TANC1 and preliminary cloning of human TANC1, which resulted in recovery of a partial cDNA. (PMID:15673434)
• mis-sense variants tested in this study may either affect protein folding or disrupt the interaction between TANC1/2 AR domains and their binding partners (PMID:31040020)
• TANC1 methylation as a novel biomarker for the diagnosis of patients with anti-tuberculosis drug-induced liver injury. (PMID:34465797)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	tanc1a	ENSDARG00000077073
mus_musculus	Tanc1	ENSMUSG00000035168
rattus_norvegicus	Tanc1	ENSRNOG00000025394

Paralogs (4): CTTNBP2 (ENSG00000077063), TANC2 (ENSG00000170921), ANKRD63 (ENSG00000230778), ANKRD65 (ENSG00000235098)

Protein

Protein identifiers

Protein TANC1 — Q9C0D5 (reviewed: Q9C0D5)

Alternative names: Tetratricopeptide repeat, ankyrin repeat and coiled-coil domain-containing protein 1

All UniProt accessions (1): Q9C0D5

UniProt curated annotations — full annotation on UniProt →

Function. May be a scaffold component in the postsynaptic density.

Subunit / interactions. Interacts probably directly with DLG1, DLG4, HOMER1. Interacts with DLGAP1, INA, CAMK2A, GRIN2B and GRIA1. Interacts with TNIK. Interacts with MINK1.

Subcellular location. Postsynaptic density.

Post-translational modifications. Phosphorylated; by MINK1 and TNIK upon stimulation by RAP2A.

Miscellaneous. Incomplete sequence.

Similarity. Belongs to the TANC family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9C0D5-1	1	yes
Q9C0D5-2	2

RefSeq proteins (6): NP_001139381, NP_001336991, NP_001336992, NP_001336993, NP_001336994, NP_203752* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002110	Ankyrin_rpt	Repeat
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR019734	TPR_rpt	Repeat
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily
IPR050889	Dendritic_Spine_Reg/Scaffold	Family
IPR058018	AAA_lid_TANC1/2	Domain
IPR058056	WH_TANC1/2	Domain

Pfam: PF00023, PF12796, PF25520, PF25521

UniProt features (45 total): repeat 14, modified residue 11, region of interest 7, compositionally biased region 7, sequence variant 4, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9C0D5-F1	62.14	0.31

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 (11): 1, 63, 66, 67, 207, 270, 465, 1439, 1668, 1676, 1677

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 224 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GOBP_COGNITION, GOBP_BEHAVIOR, GOBP_ASSOCIATIVE_LEARNING, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION, GOBP_CELLULAR_COMPONENT_MAINTENANCE, PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, FOSTER_TOLERANT_MACROPHAGE_UP, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2, GOBP_LEARNING, chr2q24, SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP

GO Biological Process (4): myoblast fusion (GO:0007520), visual learning (GO:0008542), dendritic spine maintenance (GO:0097062), regulation of postsynapse organization (GO:0099175)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (6): postsynaptic density (GO:0014069), dendrite (GO:0030425), neuronal cell body (GO:0043025), axon terminus (GO:0043679), glutamatergic synapse (GO:0098978), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
syncytium formation by cell-cell fusion	1
myotube differentiation	1
visual behavior	1
associative learning	1
cellular component maintenance	1
dendritic spine organization	1
regulation of synapse organization	1
postsynapse organization	1
binding	1
asymmetric synapse	1
postsynaptic specialization	1
neuron projection	1
dendritic tree	1
somatodendritic compartment	1
cell body	1
neuron projection terminus	1
presynapse	1
distal axon	1
synapse	1
cell junction	1

Protein interactions and networks

STRING

1340 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TANC1	INA	Q16352	778
TANC1	DLG4	P78352	701
TANC1	DLGAP1	P78335	697
TANC1	GRIN2B	Q13224	659
TANC1	GRM1	Q13255	635
TANC1	HOMER1	Q86YM7	608
TANC1	WDSUB1	Q8N9V3	592
TANC1	DLG1	Q12959	574
TANC1	CAMK2A	Q9UQM7	520
TANC1	GRIA1	P42261	491
TANC1	TNIK	Q9UKE5	472
TANC1	RBM28	Q9NW13	470
TANC1	ANAPC4	Q9UJX5	458
TANC1	COQ10B	Q9H8M1	453
TANC1	SBK1	Q52WX2	445

IntAct

177 interactions, top by confidence:

A	B	Type	Score
YWHAB	PIK3C2A	psi-mi:“MI:0914”(association)	0.800
TAX1BP3	ARVCF	psi-mi:“MI:0914”(association)	0.690
TAX1BP3	TANC1	psi-mi:“MI:0407”(direct interaction)	0.690
SCRIB	TANC1	psi-mi:“MI:0407”(direct interaction)	0.680
DLG1	TANC1	psi-mi:“MI:0407”(direct interaction)	0.680
TANC1	SCRIB	psi-mi:“MI:0407”(direct interaction)	0.680
TANC1	DLG1	psi-mi:“MI:0407”(direct interaction)	0.680
YWHAG	BLTP3B	psi-mi:“MI:0914”(association)	0.640
YWHAG	BLTP3B	psi-mi:“MI:2364”(proximity)	0.640
DLG4	TANC1	psi-mi:“MI:0407”(direct interaction)	0.620
PATJ	TANC1	psi-mi:“MI:0407”(direct interaction)	0.620
SNTB1	TANC1	psi-mi:“MI:0407”(direct interaction)	0.620
TANC1	DLG4	psi-mi:“MI:0407”(direct interaction)	0.620
TANC1	SNTB1	psi-mi:“MI:0407”(direct interaction)	0.620
TANC1	PATJ	psi-mi:“MI:0407”(direct interaction)	0.620

BioGRID (124): TANC1 (Affinity Capture-MS), TANC1 (Affinity Capture-RNA), TANC1 (Affinity Capture-RNA), TANC1 (Affinity Capture-MS), TANC1 (Proximity Label-MS), TANC1 (Proximity Label-MS), TANC1 (Proximity Label-MS), TANC1 (Proximity Label-MS), TANC1 (Affinity Capture-MS), TANC1 (Proximity Label-MS), TANC1 (Proximity Label-MS), TANC1 (Affinity Capture-RNA), TANC1 (Affinity Capture-MS), TANC1 (Proximity Label-MS), TANC1 (Proximity Label-MS)

ESM2 similar proteins: A2A2Y4, A2AFR3, A4IJ06, B9EJ86, E1C3P4, F1LXF1, G9CGD6, O08874, O14795, P49797, Q05AA6, Q0P4Q4, Q0VGY8, Q13474, Q14CM0, Q16513, Q3B7D5, Q566C5, Q5F3L9, Q5R803, Q62769, Q641K1, Q69ZK0, Q6DRP4, Q6NTL4, Q6PAJ1, Q6ZM86, Q7Z628, Q80TI0, Q8BHD4, Q8BMS9, Q8C0V9, Q8CB96, Q8IZC4, Q8K2Y9, Q8TCU6, Q923Q2, Q92625, Q96NE9, Q9BSQ5

Diamond homologs: A2A690, F1LTE0, Q0VGY8, Q38931, Q43207, Q6F6B3, Q9C0D5, Q9FJL3, Q9HCD6, A4K2V0, A6ZRW3, D7REX8, F1RBN2, F4K487, O13797, O14217, O16259, O35814, O48802, O54981, P07213, P0CT30, P15705, P25407, P31948, P38825, P53041, P53042, Q07617, Q08752, Q15785, Q2U919, Q3KRD5, Q3ZBZ8, Q4R8N7, Q54DA8, Q5U2X2, Q5VJS5, Q5WA76, Q5XEP2

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
DLG4	“up-regulates activity”	TANC1	binding
TANC1	up-regulates	Dendritic_spine_morphogenesis

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 124 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
Activation of BAD and translocation to mitochondria	7	63.4×	1e-09
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	7	56.0×	2e-09
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	56.0×	2e-09
Activation of BH3-only proteins	7	41.4×	1e-08
Ras activation upon Ca2+ influx through NMDA receptor	5	34.0×	8e-06
Signaling by Hippo	5	32.4×	9e-06
Unblocking of NMDA receptors, glutamate binding and activation	5	32.4×	9e-06
Negative regulation of NMDA receptor-mediated neuronal transmission	5	32.4×	9e-06

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	11	53.7×	4e-14
protein localization to synapse	6	38.6×	1e-06
receptor clustering	7	36.7×	2e-07
regulation of postsynaptic membrane neurotransmitter receptor levels	8	33.3×	3e-08
protein targeting	7	21.6×	3e-06
intracellular protein localization	12	10.6×	3e-07
cell-cell adhesion	12	10.2×	4e-07
protein-containing complex assembly	7	6.7×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	238
Likely benign	22
Benign	6

Top pathogenic / likely-pathogenic (0)

SpliceAI

6433 predictions. Top by Δscore:

Variant	Effect	Δscore
2:159065894:A:AG	acceptor_gain	1.0000
2:159065895:G:GG	acceptor_gain	1.0000
2:159097632:TCTA:T	acceptor_loss	1.0000
2:159097634:TAG:T	acceptor_loss	1.0000
2:159097635:A:AG	acceptor_gain	1.0000
2:159097635:AGG:A	acceptor_loss	1.0000
2:159097636:G:GG	acceptor_gain	1.0000
2:159097636:G:T	acceptor_loss	1.0000
2:159097636:GGAA:G	acceptor_gain	1.0000
2:159136294:GCATG:G	donor_gain	1.0000
2:159149285:G:GT	donor_gain	1.0000
2:159149315:G:GT	donor_gain	1.0000
2:159149322:G:GT	donor_gain	1.0000
2:159149358:G:GT	donor_gain	1.0000
2:159149358:G:T	donor_gain	1.0000
2:159149373:T:G	donor_gain	1.0000
2:159169129:GTT:G	donor_gain	1.0000
2:159169130:TTT:T	donor_gain	1.0000
2:159169131:T:G	donor_gain	1.0000
2:159169131:T:TG	donor_gain	1.0000
2:159169363:G:GT	donor_gain	1.0000
2:159170519:T:A	acceptor_gain	1.0000
2:159170522:A:AG	acceptor_gain	1.0000
2:159170523:G:GG	acceptor_gain	1.0000
2:159170523:GCA:G	acceptor_gain	1.0000
2:159170523:GCAC:G	acceptor_gain	1.0000
2:159170525:AC:A	acceptor_gain	1.0000
2:159170802:AAAA:A	donor_gain	1.0000
2:159170803:AAA:A	donor_gain	1.0000
2:159170804:AA:A	donor_gain	1.0000

AlphaMissense

12162 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:159170709:G:T	G419W	1.000
2:159170710:G:A	G419E	1.000
2:159178740:T:C	L696P	1.000
2:159178791:T:C	L713P	1.000
2:159179111:T:A	W820R	1.000
2:159179111:T:C	W820R	1.000
2:159179115:T:C	L821P	1.000
2:159185865:T:C	L862P	1.000
2:159185867:G:C	G863R	1.000
2:159185868:G:A	G863D	1.000
2:159185880:T:C	L867P	1.000
2:159185884:G:C	K868N	1.000
2:159185884:G:T	K868N	1.000
2:159186950:T:A	W890R	1.000
2:159186950:T:C	W890R	1.000
2:159194260:A:C	S916R	1.000
2:159194262:C:A	S916R	1.000
2:159194262:C:G	S916R	1.000
2:159194267:T:C	L918P	1.000
2:159194270:T:C	L919P	1.000
2:159225699:T:A	W1275R	1.000
2:159225699:T:C	W1275R	1.000
2:159225701:G:C	W1275C	1.000
2:159225701:G:T	W1275C	1.000
2:159225709:C:A	A1278D	1.000
2:159149190:T:C	L138P	0.999
2:159150551:T:C	I226T	0.999
2:159150551:T:G	I226S	0.999
2:159150554:T:A	I227K	0.999
2:159163283:C:A	A228D	0.999

dbSNP variants (sampled 300 via entrez): RS1000011850 (2:159028503 T>C,G), RS1000016670 (2:159039018 C>G,T), RS1000026109 (2:159190374 G>A,T), RS1000026489 (2:159035206 GT>G,GTT), RS1000036053 (2:159073508 A>G), RS1000057812 (2:159118621 A>G), RS1000073009 (2:159032548 G>A), RS1000080209 (2:159028928 AT>A,ATT,ATTT), RS1000095937 (2:158987331 G>T), RS1000118724 (2:159160259 G>C), RS1000134717 (2:159113460 C>A), RS1000135575 (2:159023012 G>A), RS1000158658 (2:159099090 A>G), RS1000161909 (2:159141212 C>G), RS1000165284 (2:159190352 A>G)

Disease associations

OMIM: gene MIM:611397 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): intellectual disability (MONDO:0001071)

Orphanet (1): NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

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

GWAS associations

11 associations (top):

Study	Trait	p-value
GCST002511_1	Response to radiotherapy in prostate cancer (toxicity)	5.000000e-11
GCST003542_72	Night sleep phenotypes	3.000000e-07
GCST003818_35	Resting heart rate	7.000000e-07
GCST004294_3	Nicotine dependence	2.000000e-06
GCST005042_5	Restless legs syndrome	3.000000e-25
GCST006288_273	Heel bone mineral density	8.000000e-06
GCST006288_499	Heel bone mineral density	2.000000e-09
GCST006979_43	Heel bone mineral density	3.000000e-28
GCST007277_3	Tourette syndrome	2.000000e-07
GCST008058_259	Estimated glomerular filtration rate	2.000000e-08
GCST008059_204	Estimated glomerular filtration rate	7.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007827	nighttime rest measurement
EFO:0009270	heel bone mineral density

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

7 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs10497203	Toxicity	3	radiotherapy	Prostatic Neoplasms
rs264588	Toxicity	3	radiotherapy	Prostatic Neoplasms
rs264631	Toxicity	3	radiotherapy	Prostatic Neoplasms
rs264651	Toxicity	3	radiotherapy	Prostatic Neoplasms
rs264663	Toxicity	3	radiotherapy	Prostatic Neoplasms
rs6432512	Toxicity	3	radiotherapy	Prostatic Neoplasms
rs7582141	Toxicity	3	radiotherapy	Prostatic Neoplasms

PharmGKB variants

7 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs264588	TANC1	3	1.75	1	radiotherapy
rs264631	TANC1	3	1.75	1	radiotherapy
rs264651	TANC1	3	0.00	1	radiotherapy
rs264663	TANC1	3	0.00	1	radiotherapy
rs6432512	TANC1	3	1.75	1	radiotherapy
rs7582141	TANC1	3	1.75	1	radiotherapy
rs10497203	TANC1	3	1.75	1	radiotherapy

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	6
Benzo(a)pyrene	affects methylation, decreases expression, decreases methylation	4
Tretinoin	increases expression	3
mercuric bromide	increases expression, affects cotreatment	2
Panobinostat	affects cotreatment, increases expression	2
Formaldehyde	decreases expression, increases expression	2
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tetrachlorodibenzodioxin	decreases expression	2
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, decreases methylation	1
bisphenol A	increases expression	1
trichostatin A	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
mono-(2-ethylhexyl)phthalate	increases expression	1
potassium chromate(VI)	decreases expression, affects cotreatment	1
coumarin	decreases phosphorylation	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
entinostat	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Arsenic Trioxide	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Acetaminophen	increases expression	1
Caffeine	increases phosphorylation	1
Calcitriol	decreases expression, affects cotreatment	1
Carbamazepine	affects expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT05657860	PHASE4	COMPLETED	Guanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479	PHASE4	RECRUITING	Metformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829	PHASE4	WITHDRAWN	Valbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198	PHASE4	NOT_YET_RECRUITING	Deutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736	PHASE3	COMPLETED	Clinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302	PHASE2	COMPLETED	Down Syndrome Memantine Follow-up Study
NCT03862950	PHASE2	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226	PHASE2	UNKNOWN	Study to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856	PHASE2	COMPLETED	Evaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320	PHASE1	COMPLETED	Clinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361	PHASE1	ENROLLING_BY_INVITATION	Sensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764	PHASE1	COMPLETED	Use of MRI and cTBS for Catatonia in Autism
NCT06586827	PHASE1	COMPLETED	Impact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940	PHASE1	NOT_YET_RECRUITING	Escalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT03479476	PHASE2/PHASE3	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796	PHASE1/PHASE2	COMPLETED	Effects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672	EARLY_PHASE1	RECRUITING	Clinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948	Not specified	COMPLETED	Healthy Lifestyles for People With Intellectual Disabilities
NCT01087320	Not specified	RECRUITING	Genome Medical Sequencing for Gene Discovery
NCT01652963	Not specified	UNKNOWN	Picture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395	Not specified	COMPLETED	Mental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554	Not specified	COMPLETED	Research and Characterization of New Genes Involved in Intellectual Disability
NCT01915381	Not specified	COMPLETED	Improving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623	Not specified	COMPLETED	Pivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773	Not specified	COMPLETED	Support Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849	Not specified	COMPLETED	Inter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041	Not specified	COMPLETED	Sedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438	Not specified	COMPLETED	Establishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761	Not specified	COMPLETED	Apparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420	Not specified	ACTIVE_NOT_RECRUITING	Mapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459	Not specified	ACTIVE_NOT_RECRUITING	Autism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081	Not specified	COMPLETED	Development and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502	Not specified	COMPLETED	Enhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277	Not specified	COMPLETED	Diabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754	Not specified	COMPLETED	Weight Management for Adolescents With IDD
NCT02591446	Not specified	COMPLETED	Transcranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868	Not specified	COMPLETED	Evaluation of Project TEAM (Teens Making Environmental and Activity Modifications)
NCT02721394	Not specified	UNKNOWN	FCT With Young Children With ID in the UK: A Feasibility Project V.1
NCT02746614	Not specified	COMPLETED	Psychomotor Therapy Effects in Adaptive Behavior and Motor Proficiency in Intellectual Disability
NCT02836405	Not specified	COMPLETED	TMS for the Investigation of Brain Plasticity in Autism Spectrum Disorders