AHCTF1

Summary

AHCTF1 (AT-hook containing transcription factor 1, HGNC:24618) is a protein-coding gene on chromosome 1q44, encoding Protein ELYS (Q8WYP5). Required for the assembly of a functional nuclear pore complex (NPC) on the surface of chromosomes as nuclei form at the end of mitosis. It is a common-essential gene (DepMap: required in 99.2% of cancer cell lines).

Predicted to enable DNA binding activity. Involved in nuclear pore complex assembly and regulation of cytokinesis. Located in chromosome; nuclear body; and nuclear envelope.

Source: NCBI Gene 25909 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 379 total — 5 pathogenic, 2 likely-pathogenic
• Cancer dependency (DepMap): dependent in 99.2% of screened cell lines (common-essential)
• MANE Select transcript: NM_001323342

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24618
Approved symbol	AHCTF1
Name	AT-hook containing transcription factor 1
Location	1q44
Locus type	gene with protein product
Status	Approved
Aliases	ELYS
Ensembl gene	ENSG00000153207
Ensembl biotype	protein_coding
OMIM	610853
Entrez	25909

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 7 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000326225, ENST00000366508, ENST00000470300, ENST00000477526, ENST00000483900, ENST00000498601, ENST00000648844, ENST00000916933, ENST00000916934, ENST00000944569, ENST00000944570

RefSeq mRNA: 4 — MANE Select: NM_001323342 NM_001323342, NM_001323343, NM_001410950, NM_015446

CCDS: CCDS1629, CCDS91190, CCDS91191

Canonical transcript exons

ENST00000648844 — 36 exons

Exon	Start	End
ENSE00001069246	246900337	246900469
ENSE00001069249	246900065	246900246
ENSE00001069251	246913232	246913412
ENSE00001069254	246903949	246904033
ENSE00001069255	246899451	246899512
ENSE00001069256	246905541	246905657
ENSE00001069257	246907551	246907758
ENSE00001219309	246902525	246902675
ENSE00001219334	246916142	246916395
ENSE00001860990	246931578	246931948
ENSE00003465918	246843795	246843928
ENSE00003469232	246849615	246851442
ENSE00003473992	246889966	246890059
ENSE00003478144	246867661	246867811
ENSE00003487406	246855730	246855827
ENSE00003488890	246877158	246877302
ENSE00003496036	246894659	246894748
ENSE00003497323	246898208	246898336
ENSE00003499949	246891779	246891919
ENSE00003518085	246842694	246842776
ENSE00003525846	246890956	246891060
ENSE00003529250	246853091	246853299
ENSE00003544625	246888394	246888517
ENSE00003546726	246860899	246861295
ENSE00003553614	246885493	246885680
ENSE00003567875	246887211	246887357
ENSE00003571992	246863924	246864116
ENSE00003573528	246867244	246867351
ENSE00003592573	246857691	246857814
ENSE00003605889	246876950	246877081
ENSE00003630719	246895835	246895925
ENSE00003633405	246918250	246918377
ENSE00003659691	246876037	246876187
ENSE00003677512	246888177	246888233
ENSE00003685459	246861959	246862153
ENSE00003900162	246839098	246840998

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 95.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.0456 / max 74.8246, expressed in 1715 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
18494	8.4419	1700
18495	0.4444	271
18487	0.0891	19
18491	0.0702	13

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	95.67	gold quality
calcaneal tendon	UBERON:0003701	93.37	gold quality
secondary oocyte	CL:0000655	92.79	gold quality
sperm	CL:0000019	92.41	gold quality
ventricular zone	UBERON:0003053	92.34	gold quality
Brodmann (1909) area 23	UBERON:0013554	92.29	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.62	gold quality
tendon	UBERON:0000043	91.34	gold quality
testis	UBERON:0000473	91.10	gold quality
medial globus pallidus	UBERON:0002477	91.09	gold quality
left testis	UBERON:0004533	90.88	gold quality
middle temporal gyrus	UBERON:0002771	90.83	gold quality
right testis	UBERON:0004534	90.51	gold quality
mucosa of stomach	UBERON:0001199	90.45	gold quality
pericardium	UBERON:0002407	90.29	gold quality
mucosa of paranasal sinus	UBERON:0005030	90.06	gold quality
germinal epithelium of ovary	UBERON:0001304	89.97	gold quality
parietal pleura	UBERON:0002400	89.89	gold quality
subcutaneous adipose tissue	UBERON:0002190	89.88	gold quality
male germ cell	CL:0000015	89.78	gold quality
left ovary	UBERON:0002119	89.75	gold quality
blood	UBERON:0000178	89.56	gold quality
adrenal tissue	UBERON:0018303	89.48	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.43	gold quality
oocyte	CL:0000023	89.28	gold quality
globus pallidus	UBERON:0001875	89.26	gold quality
ovary	UBERON:0000992	89.17	gold quality
right ovary	UBERON:0002118	89.17	gold quality
bone marrow	UBERON:0002371	88.89	gold quality
sural nerve	UBERON:0015488	88.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.51
E-MTAB-6379	no	1936.59

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

111 targeting AHCTF1, 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-3163	100.00	77.23	8605
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-5696	99.98	72.36	4487
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-3658	99.96	73.87	4379

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.2% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 7)

• Results suggets that ELYS is an unexpected member of the nuclear pore and kinetochore that functions in both pore assembly at the nucleus and faithful cell division. (PMID:17098863)
• ELYS/Mel28 plays a role in NE subdomain formation in late mitosis (PMID:22555603)
• These observations point to a new mechanism regulating the localization of LBR, which is governed by an ELYS-mediated phosphorylation network. (PMID:27802161)
• we identify ELYS as a novel positive effector of mammalian nuclear size and propose that nuclear size is sensitive to NPC density and nuclear import capacity. (PMID:31085625)
• AHCTF1 regulates the super-enhancer-mediated gene gating process.The cancer-cell-specific gating of MYC is regulated by AHCTF1, which connects nucleoporins to the oncogenic super-enhancer via beta-catenin. (PMID:31784729)
• Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site. (PMID:35017527)
• Phosphorylation of ELYS promotes its interaction with VAPB at decondensing chromosomes during mitosis. (PMID:38605278)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ahctf1	ENSDARG00000077530
mus_musculus	Ahctf1	ENSMUSG00000026491
rattus_norvegicus	Ahctf1	ENSRNOG00000023541
drosophila_melanogaster	Elys	FBGN0031052

Protein

Protein identifiers

Protein ELYS — Q8WYP5 (reviewed: Q8WYP5)

Alternative names: Embryonic large molecule derived from yolk sac, Protein MEL-28, Putative AT-hook-containing transcription factor 1

All UniProt accessions (2): Q8WYP5, H7C4S1

UniProt curated annotations — full annotation on UniProt →

Function. Required for the assembly of a functional nuclear pore complex (NPC) on the surface of chromosomes as nuclei form at the end of mitosis. May initiate NPC assembly by binding to chromatin and recruiting the Nup107-160 subcomplex of the NPC. Also required for the localization of the Nup107-160 subcomplex of the NPC to the kinetochore during mitosis and for the completion of cytokinesis.

Subunit / interactions. Associates with the Nup107-160 subcomplex of the NPC.

Subcellular location. Cytoplasm. Nucleus. Nucleus envelope. Nucleus matrix. Chromosome. Centromere. Kinetochore. Nucleoplasm. Nuclear pore complex.

Domain organisation. The N-terminus forms a highly conserved seven-bladed beta propeller decorated with long loops and mediates anchorage to the Nup107-160 subcomplex of the nuclear pore, synergistically with the central alpha domain. The disordered C-terminus is responsible for the interactions with chromatin.

Similarity. Belongs to the ELYS family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8WYP5-1	1	yes
Q8WYP5-2	2
Q8WYP5-3	3

RefSeq proteins (4): NP_001310271, NP_001310272, NP_001397879, NP_056261 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011047	Quinoprotein_ADH-like_sf	Homologous_superfamily
IPR025151	ELYS_dom	Domain
IPR032040	ELYS-bb	Domain
IPR052620	ELYS/MEL-28_NucAsmblyFactor	Family

Pfam: PF13934, PF16687

UniProt features (84 total): modified residue 43, sequence conflict 17, compositionally biased region 11, region of interest 7, splice variant 2, sequence variant 2, chain 1, DNA-binding region 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7R5K	ELECTRON MICROSCOPY	12
7R5J	ELECTRON MICROSCOPY	50

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WYP5-F1	55.33	0.14

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 (43): 509, 528, 1080, 1138, 1142, 1150, 1153, 1155, 1160, 1175, 1214, 1218, 1222, 1232, 1250, 1257, 1283, 1297, 1369, 1371 …

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

ID	Pathway
R-HSA-141444	Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
R-HSA-2467813	Separation of Sister Chromatids
R-HSA-2500257	Resolution of Sister Chromatid Cohesion
R-HSA-5663220	RHO GTPases Activate Formins
R-HSA-68877	Mitotic Prometaphase
R-HSA-9615933	Postmitotic nuclear pore complex (NPC) reformation
R-HSA-9648025	EML4 and NUDC in mitotic spindle formation

MSigDB gene sets: 257 (showing top): TAATAAT_MIR126, TGCACTT_MIR519C_MIR519B_MIR519A, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, BROWNE_HCMV_INFECTION_12HR_UP, GOBP_NUCLEAR_PORE_ORGANIZATION, GOBP_NUCLEAR_TRANSPORT, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_CYTOKINESIS, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_NUCLEUS_ORGANIZATION, GATA6_01, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_PORE_COMPLEX_ASSEMBLY, GOBP_REGULATION_OF_CYTOKINESIS, GOBP_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT

GO Biological Process (6): nucleocytoplasmic transport (GO:0006913), protein transport (GO:0015031), regulation of cytokinesis (GO:0032465), mRNA transport (GO:0051028), nuclear pore complex assembly (GO:0051292), cell division (GO:0051301)

GO Molecular Function (1): DNA binding (GO:0003677)

GO Cellular Component (15): kinetochore (GO:0000776), chromatin (GO:0000785), nucleus (GO:0005634), nuclear envelope (GO:0005635), nuclear pore (GO:0005643), nucleoplasm (GO:0005654), cytosol (GO:0005829), nuclear matrix (GO:0016363), nuclear body (GO:0016604), nuclear membrane (GO:0031965), extracellular exosome (GO:0070062), chromosome, centromeric region (GO:0000775), chromosome (GO:0005694), cytoplasm (GO:0005737), nuclear pore outer ring (GO:0031080)

Reactome top-level categories

Rollup of top-6 pathways:

Category	Pathways
Mitotic Prometaphase	2
Amplification of signal from the kinetochores	1
Mitotic Anaphase	1
RHO GTPase Effectors	1
M Phase	1
Nuclear Envelope (NE) Reassembly	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
intracellular membraneless organelle	3
nucleus	2
nuclear envelope	2
nuclear protein-containing complex	2
nuclear lumen	2
nuclear transport	1
transport	1
intracellular protein localization	1
establishment of protein localization	1
cytokinesis	1
regulation of cell cycle process	1
regulation of cell division	1
RNA transport	1
nuclear pore organization	1
pore complex assembly	1
cellular process	1
nucleic acid binding	1
condensed chromosome, centromeric region	1
supramolecular complex	1
chromosome	1
intracellular membrane-bounded organelle	1
endomembrane system	1
organelle envelope	1
cytoplasm	1
nucleoplasm	1
organelle membrane	1
extracellular vesicle	1
chromosomal region	1
intracellular anatomical structure	1
nuclear pore	1

Protein interactions and networks

STRING

1432 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
AHCTF1	NUP160	Q12769	996
AHCTF1	NUP133	Q8WUM0	990
AHCTF1	NUP107	P57740	989
AHCTF1	NUP37	Q8NFH4	977
AHCTF1	NUP153	P49790	971
AHCTF1	SEC13	P55735	969
AHCTF1	NUP43	Q8NFH3	953
AHCTF1	SEH1L	Q96EE3	944
AHCTF1	RANBP2	P49792	916
AHCTF1	NUP98	P52948	916
AHCTF1	NUP85	Q9BW27	888
AHCTF1	NUP50	Q9UKX7	876
AHCTF1	NUP62	P37198	840
AHCTF1	NUP93	Q8N1F7	835
AHCTF1	NUP214	P35658	811

IntAct

118 interactions, top by confidence:

A	B	Type	Score
MED19	MED19	psi-mi:“MI:0914”(association)	0.730
VAPB	FAM83G	psi-mi:“MI:0914”(association)	0.730
VAPA	FAM83G	psi-mi:“MI:0914”(association)	0.640
VAPA	PITPNM1	psi-mi:“MI:0914”(association)	0.640
IL13RA2	METTL15	psi-mi:“MI:0914”(association)	0.530
LAMP3	METTL15	psi-mi:“MI:0914”(association)	0.530
ISLR	BCKDK	psi-mi:“MI:0914”(association)	0.530
STK16	UNC119B	psi-mi:“MI:0914”(association)	0.530
CD70	METTL15	psi-mi:“MI:0914”(association)	0.530
TNFSF8	LGALS8	psi-mi:“MI:0914”(association)	0.530
AHCTF1	NUP98	psi-mi:“MI:0915”(physical association)	0.490
DDX21	MED19	psi-mi:“MI:2364”(proximity)	0.480
Nanog	Sp1	psi-mi:“MI:0914”(association)	0.460
AHCTF1	PLEC	psi-mi:“MI:0915”(physical association)	0.400
AHCTF1	KRT8	psi-mi:“MI:0915”(physical association)	0.400
AHCTF1	VIM	psi-mi:“MI:0915”(physical association)	0.400
AHCTF1	KRT18	psi-mi:“MI:0915”(physical association)	0.400
AHCTF1	HMGN3	psi-mi:“MI:0915”(physical association)	0.400
Nup98	NUP98	psi-mi:“MI:0915”(physical association)	0.400
NUP85	NUP98	psi-mi:“MI:0915”(physical association)	0.400
AHCTF1	NUP155	psi-mi:“MI:0915”(physical association)	0.400
Nup98	POM121C	psi-mi:“MI:0914”(association)	0.350
Nup107	POM121C	psi-mi:“MI:0914”(association)	0.350
NPM1	RPSA	psi-mi:“MI:0914”(association)	0.350
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350
Prdm16	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (200): AHCTF1 (Affinity Capture-RNA), AHCTF1 (Affinity Capture-RNA), AHCTF1 (Affinity Capture-RNA), AHCTF1 (Affinity Capture-MS), AHCTF1 (Affinity Capture-MS), AHCTF1 (Affinity Capture-MS), AHCTF1 (Affinity Capture-MS), AHCTF1 (Affinity Capture-MS), AHCTF1 (Affinity Capture-MS), AHCTF1 (Co-fractionation), AHCTF1 (Affinity Capture-MS), AHCTF1 (Proximity Label-MS), AHCTF1 (Proximity Label-MS), AHCTF1 (Proximity Label-MS), AHCTF1 (Proximity Label-MS)

ESM2 similar proteins: A0A0R4IC37, A1A4K3, A2CEI4, B1WC10, E9PY46, F1QEB7, F4IDS7, O08658, O13046, O75694, O75717, O95876, P33194, P37199, P59328, Q08D69, Q10569, Q10570, Q16531, Q32NR9, Q3U1J4, Q4ADV7, Q566H4, Q5DQR4, Q5R649, Q5U1Z0, Q5ZLG9, Q6P6Z0, Q6PGF3, Q6PJI9, Q7XWP1, Q802U2, Q805F9, Q8BMG7, Q8C0M0, Q8C456, Q8CEC0, Q8CJF7, Q8K1X1, Q8NFP9

Diamond homologs: Q5U249, Q8CJF7, Q8WYP5

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
AHCTF1	“form complex”	NPC	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 151 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
Nuclear import of Rev protein	6	20.6×	1e-04
Vpr-mediated nuclear import of PICs	6	20.6×	1e-04
IPs transport between nucleus and cytosol	5	19.4×	4e-04
IP3 and IP4 transport between cytosol and nucleus	5	19.4×	4e-04
IP6 and IP7 transport between cytosol and nucleus	5	19.4×	4e-04
Transport of Ribonucleoproteins into the Host Nucleus	5	18.2×	4e-04
Regulation of Glucokinase by Glucokinase Regulatory Protein	5	18.2×	4e-04
Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC)	5	18.2×	4e-04

GO biological processes:

GO term	Partners	Fold	FDR
RNA export from nucleus	5	35.5×	2e-04
nucleocytoplasmic transport	5	14.8×	5e-03
mRNA transport	6	12.0×	4e-03
protein import into nucleus	7	7.6×	8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	5
Likely pathogenic	2
Uncertain significance	294
Likely benign	30
Benign	0

Top pathogenic / likely-pathogenic (7)

Variant ID	HGVS	Classification
144382	GRCh38/hg38 1q44(chr1:245312815-248918469)x3	Pathogenic
146306	GRCh38/hg38 1q44(chr1:244582123-248918469)x1	Pathogenic
1710923	GRCh37/hg19 1q44(chr1:246850401-249205263)x3	Pathogenic
565250	GRCh37/hg19 1q44(chr1:244797639-249224684)x1	Pathogenic
687454	GRCh37/hg19 1q44(chr1:246565044-249224684)x1	Pathogenic
625535	GRCh37/hg19 1q44(chr1:245341153-249212429)	Likely pathogenic
980425	GRCh37/hg19 1q44(chr1:246853199-249181899)x1	Likely pathogenic

SpliceAI

5145 predictions. Top by Δscore:

Variant	Effect	Δscore
1:246840994:TGTTT:T	acceptor_gain	1.0000
1:246840996:TTT:T	acceptor_gain	1.0000
1:246840997:TT:T	acceptor_gain	1.0000
1:246840999:C:CC	acceptor_gain	1.0000
1:246842692:A:AC	donor_gain	1.0000
1:246842693:C:CC	donor_gain	1.0000
1:246842693:CTTG:C	donor_gain	1.0000
1:246842696:G:GC	donor_gain	1.0000
1:246842697:C:CC	donor_gain	1.0000
1:246842697:CTTG:C	donor_gain	1.0000
1:246843870:C:CC	acceptor_gain	1.0000
1:246843929:C:CC	acceptor_gain	1.0000
1:246849624:T:A	donor_gain	1.0000
1:246851439:TCAC:T	acceptor_gain	1.0000
1:246851440:CAC:C	acceptor_gain	1.0000
1:246851440:CACC:C	acceptor_gain	1.0000
1:246851441:ACC:A	acceptor_loss	1.0000
1:246851442:CCTA:C	acceptor_loss	1.0000
1:246853086:TTTAC:T	donor_loss	1.0000
1:246853087:TTACA:T	donor_loss	1.0000
1:246853088:TACAT:T	donor_loss	1.0000
1:246853089:A:AC	donor_gain	1.0000
1:246853089:AC:A	donor_loss	1.0000
1:246853090:C:CC	donor_gain	1.0000
1:246853090:CATGA:C	donor_gain	1.0000
1:246853158:T:A	donor_gain	1.0000
1:246853182:T:TA	donor_gain	1.0000
1:246853212:T:TA	donor_gain	1.0000
1:246853295:CATAG:C	acceptor_gain	1.0000
1:246853296:ATAG:A	acceptor_gain	1.0000

AlphaMissense

14752 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:246900368:A:G	W407R	1.000
1:246900368:A:T	W407R	1.000
1:246900352:A:G	M412T	0.999
1:246900366:C:A	W407C	0.999
1:246900366:C:G	W407C	0.999
1:246905566:A:G	W286R	0.999
1:246905566:A:T	W286R	0.999
1:246905589:T:C	D278G	0.999
1:246900365:A:G	Y408H	0.998
1:246900379:T:A	D403V	0.998
1:246900382:A:G	F402S	0.998
1:246900434:A:G	W385R	0.998
1:246900434:A:T	W385R	0.998
1:246900450:A:C	S379R	0.998
1:246900450:A:T	S379R	0.998
1:246900452:T:G	S379R	0.998
1:246904007:A:G	L303P	0.998
1:246905589:T:A	D278V	0.998
1:246905598:G:T	P275H	0.998
1:246876987:G:T	A967D	0.997
1:246877011:A:G	L959S	0.997
1:246888414:A:G	Y750H	0.997
1:246888444:A:G	W740R	0.997
1:246888444:A:T	W740R	0.997
1:246900206:A:G	W431R	0.997
1:246900206:A:T	W431R	0.997
1:246900359:C:G	A410P	0.997
1:246900365:A:C	Y408D	0.997
1:246900367:C:G	W407S	0.997
1:246900370:C:G	R406P	0.997

dbSNP variants (sampled 300 via entrez): RS1000015874 (1:246880063 G>C), RS1000017913 (1:246897131 T>A,G), RS1000079508 (1:246843684 TAAAC>T), RS1000107451 (1:246874539 T>A,C), RS1000123882 (1:246883803 C>G), RS1000136522 (1:246924565 C>T), RS1000166306 (1:246930972 G>A), RS1000182136 (1:246893733 G>C), RS1000214730 (1:246893395 A>C,G), RS1000234055 (1:246902900 TATTTAAC>T), RS1000247869 (1:246854590 T>C), RS1000255015 (1:246921294 G>A), RS1000323967 (1:246847168 A>G), RS1000365940 (1:246838858 T>C), RS1000368199 (1:246869153 T>C)

Disease associations

OMIM: gene MIM:610853 | disease phenotypes:

GenCC curated gene-disease

Mondo (3): primary amenorrhea (MONDO:1060208), intellectual disability (MONDO:0001071), strabismus (MONDO:0003432)

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

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST012490_272	Femur bone mineral density x serum urate levels interaction	3.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004531	urate measurement

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D013285	Strabismus	C10.292.562.887; C11.590.810

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	3
Valproic Acid	decreases expression, increases expression, increases methylation	3
Endosulfan	decreases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
FR900359	affects phosphorylation	1
alpha-pinene	decreases expression, increases abundance, affects cotreatment	1
bisphenol A	decreases expression	1
geraniol	decreases expression	1
testosterone undecanoate	affects cotreatment, increases expression	1
arsenite	affects binding, decreases reaction	1
coumarin	affects phosphorylation	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
pinostrobin	increases phosphorylation	1
torcetrapib	increases expression	1
ICG 001	increases expression	1
jinfukang	decreases expression	1
NSC 689534	decreases expression, affects binding	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Acrolein	affects cotreatment, decreases expression, increases abundance	1
Air Pollutants	affects cotreatment, decreases expression, increases abundance	1
Arsenic	affects expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	increases mutagenesis	1
Caffeine	affects phosphorylation	1
Copper	affects binding, decreases expression	1

Cellosaurus cell lines

16 cell lines: 16 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_0179	BT-474	Cancer cell line	Female
CVCL_4V65	BT474-5FU[r]	Cancer cell line	Female
CVCL_4Y08	BT-474/CMV-Luc	Cancer cell line	Female
CVCL_A2GH	LR-BT474	Cancer cell line	Female
CVCL_A4AK	BT-474 Tam2	Cancer cell line	Female
CVCL_A4CL	BT-474 Ecadherin EmGFP	Cancer cell line	Female
CVCL_AQ07	BT-474 Clone 5	Cancer cell line	Female
CVCL_AR86	BT-474 Tam1	Cancer cell line	Female
CVCL_AR96	BT-474 EEI	Cancer cell line	Female
CVCL_C9CU	BT-474-Luc2	Cancer cell line	Female

Clinical trials (associated diseases)

300 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
NCT00461656	PHASE4	COMPLETED	Povidone-iodine Antisepsis for Strabismus Surgery
NCT01901588	PHASE4	COMPLETED	Efficacy of Single-Shot Dexmedetomidine Versus Placebo in Preventing Pediatric Emergence Delirium in Strabismus Surgery
NCT02379546	PHASE4	COMPLETED	The Effect of Anaesthesia Depth on Oculo-cardiac Reflex
NCT03349515	PHASE4	COMPLETED	The Effect of Povidone-iodine Ophthalmic Surgical Prep Solution on Respiration in Children Undergoing Strabismus Surgery With General Anesthesia.
NCT04549844	PHASE4	UNKNOWN	Peribulbar Block for Prevention of Oculocardiac Reflex
NCT06035757	PHASE4	RECRUITING	The Occurrence of Emergence Agitation in Pediatric Strabismus Surgery
NCT06560268	PHASE4	NOT_YET_RECRUITING	Low Flow Anesthesia in Children Undergoing Strabismus Surgery
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
NCT00000128	PHASE3	UNKNOWN	A Trial of Bifocals in Myopic Children With Esophoria
NCT00001864	PHASE3	COMPLETED	Amblyopia (Lazy Eye) Treatment Study
NCT00038753	PHASE3	UNKNOWN	Vision In Preschoolers Study (VIP Study)
NCT01584843	PHASE3	COMPLETED	Efficacy and Safety of GSK1358820 (Botulinum Toxin Type A) in Patients With Strabismus
NCT04060771	PHASE3	UNKNOWN	Post-Operative Nausea and Vomiting in Children Submitted to Strabismus Surgery
NCT06863675	PHASE3	NOT_YET_RECRUITING	Highly Aspherical Lenslet (HAL) and Binocular Vision (BV) Disorders [HALT X(T) Study]
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
NCT00478907	PHASE2	COMPLETED	Prevention of Complications of Eye Surgery
NCT06689943	PHASE2	NOT_YET_RECRUITING	Pain After Strabismus Surgery
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)
NCT00917982	PHASE1	UNKNOWN	The Effect of Vision Therapy/Orthoptic on Motor & Sensory Status of the 3 to 7 Years Old Strabismic Patients
NCT02246556	PHASE1	TERMINATED	Dichoptic Virtual Reality Therapy for Amblyopia in Adults
NCT07164248	Not specified	COMPLETED	Evaluation of Bone Mineral Density Indications and Outcomes in Female Adolescents: Implications for Early Detection of Osteopenia/Osteoporosis and Gynecologic Practice
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