KCTD3

Summary

KCTD3 (potassium channel tetramerization domain containing 3, HGNC:21305) is a protein-coding gene on chromosome 1q41, encoding BTB/POZ domain-containing protein KCTD3 (Q9Y597). Accessory subunit of potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 (HCN3) up-regulating its cell-surface expression and current density without affecting its voltage dependence and kinetics.

This gene encodes a member of the potassium channel tetramerization-domain containing (KCTD) protein family. Members of this protein family regulate the biophysical characteristics of ion channels. In mouse, this protein interacts with hyperpolarization-activated cyclic nucleotide-gated channel complex 3 and enhances its cell surface expression and current density. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 51133 — RefSeq curated summary.

At a glance

• Gene–disease (curated): neurodevelopmental disorder (Strong, GenCC)
• GWAS associations: 1
• Clinical variants (ClinVar): 117 total — 2 pathogenic
• Phenotypes (HPO): 1
• MANE Select transcript: NM_016121

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21305
Approved symbol	KCTD3
Name	potassium channel tetramerization domain containing 3
Location	1q41
Locus type	gene with protein product
Status	Approved
Aliases	NY-REN-45
Ensembl gene	ENSG00000136636
Ensembl biotype	protein_coding
OMIM	613272
Entrez	51133

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 18 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000259154, ENST00000448333, ENST00000452413, ENST00000465650, ENST00000495537, ENST00000905624, ENST00000905625, ENST00000905626, ENST00000905627, ENST00000905628, ENST00000905629, ENST00000905630, ENST00000905631, ENST00000919549, ENST00000919550, ENST00000964519, ENST00000964520, ENST00000964521, ENST00000964522, ENST00000964523

RefSeq mRNA: 3 — MANE Select: NM_016121 NM_001319294, NM_001319295, NM_016121

CCDS: CCDS1515

Canonical transcript exons

ENST00000259154 — 18 exons

Exon	Start	End
ENSE00000925560	215608017	215608172
ENSE00000925561	215611825	215611921
ENSE00001153973	215618886	215619070
ENSE00002322242	215604132	215604302
ENSE00002332760	215575901	215575974
ENSE00002335312	215595356	215595471
ENSE00002366930	215577670	215577728
ENSE00002375239	215578001	215578081
ENSE00002378785	215573786	215573839
ENSE00002386877	215586495	215586685
ENSE00002396191	215602085	215602201
ENSE00002400051	215579000	215579137
ENSE00002400381	215601867	215601954
ENSE00002412930	215579909	215579999
ENSE00002421165	215574073	215574118
ENSE00002711367	215567304	215567768
ENSE00003241167	215620057	215621807
ENSE00003563016	215619153	215619291

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 97.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.7370 / max 167.3061, expressed in 1782 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
8580	13.4157	1755
8578	7.8770	1590
8579	0.3410	161
8582	0.1033	29

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
jejunal mucosa	UBERON:0000399	97.54	gold quality
right adrenal gland cortex	UBERON:0035827	97.23	gold quality
right adrenal gland	UBERON:0001233	96.76	gold quality
left adrenal gland	UBERON:0001234	96.44	gold quality
adrenal cortex	UBERON:0001235	96.41	gold quality
left adrenal gland cortex	UBERON:0035825	96.28	gold quality
adrenal gland	UBERON:0002369	95.96	gold quality
ventricular zone	UBERON:0003053	95.21	gold quality
adrenal tissue	UBERON:0018303	94.80	gold quality
cerebellar cortex	UBERON:0002129	94.39	gold quality
cerebellar hemisphere	UBERON:0002245	94.38	gold quality
vagina	UBERON:0000996	94.29	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	94.27	gold quality
muscle layer of sigmoid colon	UBERON:0035805	94.25	gold quality
peripheral nervous system	UBERON:0000010	93.90	gold quality
nerve	UBERON:0001021	93.90	gold quality
tibial nerve	UBERON:0001323	93.90	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.86	gold quality
spinal cord	UBERON:0002240	93.58	gold quality
stromal cell of endometrium	CL:0002255	93.55	gold quality
cerebellum	UBERON:0002037	93.38	gold quality
body of pancreas	UBERON:0001150	93.24	gold quality
ganglionic eminence	UBERON:0004023	93.13	gold quality
duodenum	UBERON:0002114	93.01	gold quality
right lobe of liver	UBERON:0001114	92.91	gold quality
calcaneal tendon	UBERON:0003701	92.61	gold quality
esophagus mucosa	UBERON:0002469	92.55	gold quality
caput epididymis	UBERON:0004358	92.42	gold quality
ectocervix	UBERON:0012249	92.26	gold quality
corpus epididymis	UBERON:0004359	92.25	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

65 targeting KCTD3, 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-3646	100.00	73.56	5283
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-4262	100.00	73.26	3931
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-MIR-150-5P	99.99	66.69	1976
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-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-5682	99.89	72.56	1005

Literature-anchored findings (GeneRIF, showing 2)

• KCTD3 is an accessory subunit of native HCN3 complexes (PMID:23382386)
• this largest series to date on KCTD3-mutated patients, we show that biallelic loss of function mutations in KCTD3 lead to a consistent phenotype of developmental epileptic encephalopathy and abnormal cerebellum on brain imaging. (PMID:29406573)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	kctd3	ENSDARG00000060854
mus_musculus	Kctd3	ENSMUSG00000026608
rattus_norvegicus	Kctd3	ENSRNOG00000002627
drosophila_melanogaster	CG9467	FBGN0037758
caenorhabditis_elegans		WBGENE00020721

Paralogs (1): SHKBP1 (ENSG00000160410)

Protein

Protein identifiers

BTB/POZ domain-containing protein KCTD3 — Q9Y597 (reviewed: Q9Y597)

Alternative names: Renal carcinoma antigen NY-REN-45

All UniProt accessions (3): Q9Y597, H0Y566, H0Y5P8

UniProt curated annotations — full annotation on UniProt →

Function. Accessory subunit of potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 (HCN3) up-regulating its cell-surface expression and current density without affecting its voltage dependence and kinetics.

Subunit / interactions. Interacts with HCN3.

Subcellular location. Cell membrane.

Tissue specificity. Broadly expressed in normal tissues.

Miscellaneous. Reacts with sera from 5-25 per cent of cancer patients but not with sera from normal donors. Seventy per cent of renal cancer patients have antibodies against one or a panel of these antigens.

Similarity. Belongs to the KCTD3 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9Y597-1	1	yes
Q9Y597-2	2
Q9Y597-3	3

RefSeq proteins (3): NP_001306223, NP_001306224, NP_057205* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000210	BTB/POZ_dom	Domain
IPR001680	WD40_rpt	Repeat
IPR003131	T1-type_BTB	Domain
IPR011333	SKP1/BTB/POZ_sf	Homologous_superfamily
IPR015943	WD40/YVTN_repeat-like_dom_sf	Homologous_superfamily
IPR036322	WD40_repeat_dom_sf	Homologous_superfamily
IPR047825	SHKBP1_KCTD3_BTB_POZ	Domain
IPR047876	SHKBP1/KCTD3	Family

Pfam: PF02214

UniProt features (27 total): repeat 8, modified residue 4, sequence conflict 4, region of interest 3, compositionally biased region 3, splice variant 2, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y597-F1	70.88	0.43

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 (4): 604, 664, 711, 793

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-9013148	CDC42 GTPase cycle
R-HSA-162582	Signal Transduction
R-HSA-194315	Signaling by Rho GTPases
R-HSA-9012999	RHO GTPase cycle
R-HSA-9716542	Signaling by Rho GTPases, Miro GTPases and RHOBTB3

MSigDB gene sets: 129 (showing top): GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, SMID_BREAST_CANCER_LUMINAL_B_UP, PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP, BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP, DODD_NASOPHARYNGEAL_CARCINOMA_UP, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, GOBP_PROTEIN_HOMOOLIGOMERIZATION, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, ACEVEDO_LIVER_CANCER_UP, CHANDRAN_METASTASIS_TOP50_DN, NUYTTEN_EZH2_TARGETS_DN, RHEIN_ALL_GLUCOCORTICOID_THERAPY_DN, COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP, OKUMURA_INFLAMMATORY_RESPONSE_LPS, GOBP_PROTEIN_COMPLEX_OLIGOMERIZATION

GO Biological Process (1): protein homooligomerization (GO:0051260)

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

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
RHO GTPase cycle	1
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	1
Signaling by Rho GTPases	1
Signal Transduction	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein complex oligomerization	1
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

722 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KCTD3	USH2A	O75445	790
KCTD3	CNTNAP2	Q9UHC6	777
KCTD3	HCN3	Q9P1Z3	688
KCTD3	KCTD19	Q17RG1	645
KCTD3	KCTD11	Q693B1	625
KCTD3	SPATA17	Q96L03	559
KCTD3	GPATCH2	Q9NW75	532
KCTD3	KCTD20	Q7Z5Y7	528
KCTD3	KCNA2	P16389	524
KCTD3	KCTD13	Q8WZ19	518
KCTD3	NRXN2	Q9P2S2	493
KCTD3	NXN	Q6DKJ4	490
KCTD3	RRP15	Q9Y3B9	474
KCTD3	FBXW8	Q8N3Y1	470
KCTD3	FAM110A	Q9BQ89	463
KCTD3	BTBD10	Q9BSF8	463

IntAct

282 interactions, top by confidence:

A	B	Type	Score
PTPN3	YWHAQ	psi-mi:“MI:2364”(proximity)	0.850
SHKBP1	CUL3	psi-mi:“MI:0914”(association)	0.850
NHERF2	PODXL	psi-mi:“MI:0914”(association)	0.770
KCTD3	PTPN3	psi-mi:“MI:0407”(direct interaction)	0.710
SNX27	MCC	psi-mi:“MI:0914”(association)	0.700
PTPN3	MCC	psi-mi:“MI:0914”(association)	0.660
PTPN3	ACOT8	psi-mi:“MI:0914”(association)	0.590
CUL3	RHOBTB1	psi-mi:“MI:0914”(association)	0.530
CUL3	ZSWIM8	psi-mi:“MI:0914”(association)	0.530
WDR83	SH2B2	psi-mi:“MI:0914”(association)	0.530
UBE2M	RHOBTB1	psi-mi:“MI:0914”(association)	0.530
SHKBP1	ASPSCR1	psi-mi:“MI:0914”(association)	0.530
GPS1	PXDNL	psi-mi:“MI:0914”(association)	0.530
YWHAB	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
KCTD3	FRMPD4	psi-mi:“MI:0407”(direct interaction)	0.440
KCTD3	PARD3	psi-mi:“MI:0407”(direct interaction)	0.440
KCTD3	MAST2	psi-mi:“MI:0407”(direct interaction)	0.440
KCTD3	MPP7	psi-mi:“MI:0407”(direct interaction)	0.440
HTRA1	KCTD3	psi-mi:“MI:0407”(direct interaction)	0.440
KCTD3	ARHGEF11	psi-mi:“MI:0407”(direct interaction)	0.440
KCTD3	APBA3	psi-mi:“MI:0407”(direct interaction)	0.440
AHNAK	KCTD3	psi-mi:“MI:0407”(direct interaction)	0.440
KCTD3	APBA2	psi-mi:“MI:0407”(direct interaction)	0.440
KCTD3	ARHGAP21	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (218): KCTD3 (Affinity Capture-MS), KCTD3 (Affinity Capture-MS), KCTD3 (Affinity Capture-MS), KCTD3 (Affinity Capture-MS), KCTD3 (Affinity Capture-MS), KCTD3 (Affinity Capture-MS), KCTD3 (Affinity Capture-MS), KCTD3 (Two-hybrid), KCTD3 (Affinity Capture-MS), KCTD3 (Affinity Capture-MS), KCTD3 (Affinity Capture-MS), KCTD3 (Affinity Capture-MS), KCTD3 (Affinity Capture-MS), KCTD3 (Affinity Capture-MS), SHKBP1 (Affinity Capture-MS)

ESM2 similar proteins: A0A078CGE6, A2QHV0, A7KAX9, A7SNN5, A9RVK2, B0XPE7, B5X564, D0Z5N4, F4HYG2, F4I114, F4IRW0, F4J394, F4J6F6, F4JY37, O00444, O13839, O24527, O43065, P0CP71, P13185, P38623, P42858, P50526, Q03407, Q0CL79, Q0WPH8, Q14693, Q19192, Q2KHT3, Q2QAV0, Q4WJI7, Q5B4Z3, Q5R9Z7, Q60DG4, Q6GPD0, Q6H647, Q756Z0, Q75CH3, Q75DK7, Q75QN6

Diamond homologs: A3KMV1, A4IFB4, A5PKG7, A6H6X4, B1WC97, B5DEL1, D5SHR0, G5EFC3, O65555, P0C5J9, P15388, P17971, P17972, P25122, P48547, P59994, P59995, Q01956, Q03607, Q03719, Q0VD00, Q0VFV7, Q14003, Q14681, Q29RJ0, Q2HJ48, Q2TUM3, Q3URF8, Q4G0X4, Q50H33, Q52PG9, Q54KH0, Q5DTY9, Q5M956, Q5XJ34, Q5ZJP7, Q62897, Q63881, Q63959, Q68DU8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 206 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
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	5	24.5×	1e-04
DNA Damage Recognition in GG-NER	7	14.6×	7e-05
RHOQ GTPase cycle	11	14.6×	1e-07
RND3 GTPase cycle	6	11.4×	7e-04
Assembly and cell surface presentation of NMDA receptors	6	11.1×	7e-04
MAP2K and MAPK activation	5	10.4×	3e-03
RHOU GTPase cycle	5	10.2×	3e-03
Neurexins and neuroligins	7	10.1×	4e-04

GO biological processes:

GO term	Partners	Fold	FDR
protein neddylation	9	33.4×	3e-09
regulation of protein neddylation	6	29.7×	2e-05
protein localization to synapse	5	20.3×	6e-04
establishment or maintenance of epithelial cell apical/basal polarity	6	18.4×	2e-04
regulation of postsynaptic membrane neurotransmitter receptor levels	6	15.7×	3e-04
establishment of cell polarity	7	14.2×	2e-04
establishment of protein localization	5	11.4×	5e-03
protein homotetramerization	6	7.5×	8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	82
Likely benign	7
Benign	2

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
2303343	NM_016121.5(KCTD3):c.648G>A (p.Trp216Ter)	Pathogenic
833117	NC_000001.10:g.(?215747129)(215824143_?)del	Pathogenic

SpliceAI

2907 predictions. Top by Δscore:

Variant	Effect	Δscore
1:215574071:A:AG	acceptor_gain	1.0000
1:215574072:G:GG	acceptor_gain	1.0000
1:215575896:TACAG:T	acceptor_gain	1.0000
1:215575897:A:AG	acceptor_gain	1.0000
1:215575897:ACAGA:A	acceptor_gain	1.0000
1:215575898:C:G	acceptor_gain	1.0000
1:215575898:CAGA:C	acceptor_gain	1.0000
1:215575899:A:AG	acceptor_gain	1.0000
1:215575899:A:G	acceptor_loss	1.0000
1:215575899:AGAT:A	acceptor_gain	1.0000
1:215575900:G:GC	acceptor_gain	1.0000
1:215575900:GA:G	acceptor_gain	1.0000
1:215575900:GAT:G	acceptor_gain	1.0000
1:215575900:GATA:G	acceptor_gain	1.0000
1:215575900:GATAT:G	acceptor_gain	1.0000
1:215575970:TTAAG:T	donor_gain	1.0000
1:215575972:AAGG:A	donor_loss	1.0000
1:215575973:AG:A	donor_gain	1.0000
1:215575973:AGGT:A	donor_loss	1.0000
1:215575974:GG:G	donor_gain	1.0000
1:215575975:G:GG	donor_gain	1.0000
1:215577668:A:AG	acceptor_gain	1.0000
1:215577668:AGG:A	acceptor_gain	1.0000
1:215577669:G:GG	acceptor_gain	1.0000
1:215577669:GGG:G	acceptor_gain	1.0000
1:215578996:A:AG	acceptor_gain	1.0000
1:215578996:ATAG:A	acceptor_gain	1.0000
1:215578997:T:G	acceptor_gain	1.0000
1:215578998:A:AG	acceptor_gain	1.0000
1:215578998:AG:A	acceptor_gain	1.0000

AlphaMissense

5311 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:215567744:T:A	V20D	1.000
1:215567750:T:A	L22Q	1.000
1:215567750:T:C	L22P	1.000
1:215567754:C:A	N23K	1.000
1:215567754:C:G	N23K	1.000
1:215567756:T:A	V24E	1.000
1:215567758:G:A	G25R	1.000
1:215567758:G:C	G25R	1.000
1:215567758:G:T	G25W	1.000
1:215567759:G:A	G25E	1.000
1:215567759:G:T	G25V	1.000
1:215567761:G:A	G26R	1.000
1:215567761:G:C	G26R	1.000
1:215567761:G:T	G26W	1.000
1:215567762:G:A	G26E	1.000
1:215567762:G:T	G26V	1.000
1:215573787:T:C	F29L	1.000
1:215573788:T:C	F29S	1.000
1:215573788:T:G	F29C	1.000
1:215573789:T:A	F29L	1.000
1:215573789:T:G	F29L	1.000
1:215573794:C:T	T31I	1.000
1:215573806:C:T	T35I	1.000
1:215573809:T:A	L36H	1.000
1:215573809:T:C	L36P	1.000
1:215573826:T:C	S42P	1.000
1:215573827:C:A	S42Y	1.000
1:215573827:C:T	S42F	1.000
1:215573829:T:C	F43L	1.000
1:215573830:T:C	F43S	1.000

dbSNP variants (sampled 300 via entrez): RS1000006835 (1:215580835 A>T), RS1000073575 (1:215591149 G>A,T), RS1000159114 (1:215611225 A>T), RS1000182976 (1:215606247 A>G), RS1000203693 (1:215566167 C>T), RS1000207460 (1:215597784 A>G,T), RS1000218524 (1:215617403 A>G), RS1000278787 (1:215572034 T>C), RS1000296307 (1:215601013 C>G,T), RS1000423609 (1:215591360 T>C), RS1000446060 (1:215578889 G>A,T), RS1000447811 (1:215581031 A>G,T), RS1000557910 (1:215621496 A>G,T), RS1000646450 (1:215570081 A>G), RS1000722384 (1:215565946 T>C)

Disease associations

OMIM: gene MIM:613272 | disease phenotypes: MIM:213000, MIM:612100, MIM:209850, MIM:276901, MIM:613809

GenCC curated gene-disease

Disease	Classification	Inheritance
neurodevelopmental disorder	Strong	Autosomal recessive

Mondo (7): isolated cerebellar hypoplasia/agenesis (MONDO:0008939), autism, susceptibility to, 15 (MONDO:0012801), breast ductal adenocarcinoma (MONDO:0005590), autism (MONDO:0005260), Usher syndrome type 2A (MONDO:0010169), retinitis pigmentosa 39 (MONDO:0013436), neurodevelopmental disorder (MONDO:0700092)

Orphanet (5): Isolated cerebellar agenesis (Orphanet:1398), Cerebellar hypoplasia-tapetoretinal degeneration syndrome (Orphanet:2246), Usher syndrome type 2 (Orphanet:231178), Retinitis pigmentosa (Orphanet:791), Usher syndrome (Orphanet:886)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0000717	Autism

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST005830_76	Hand grip strength	7.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006941	grip strength measurement

MeSH disease descriptors (5)

Descriptor	Name	Tree numbers
D001321	Autistic Disorder	F03.625.164.113.500
D018270	Carcinoma, Ductal, Breast	C04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390
D065886	Neurodevelopmental Disorders	F03.625
C562568	Cerebellar Hypoplasia (supp.)
C536490	Usher syndrome, type 2A (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Cadmium Chloride	decreases expression	2
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
sodium arsenite	decreases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	decreases methylation	1
coumarin	affects phosphorylation	1
perfluorooctane sulfonic acid	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Azathioprine	decreases expression	1
Benzo(a)pyrene	decreases expression	1
Caffeine	affects phosphorylation	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	decreases expression	1
Formaldehyde	decreases expression	1
Methapyrilene	increases methylation	1
Methyl Methanesulfonate	decreases expression	1
Methylcholanthrene	affects binding, increases reaction	1
Dihydrotestosterone	increases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	affects expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	decreases expression	1
Fenretinide	decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1
Topotecan	affects response to substance	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04586348	PHASE4	UNKNOWN	Prenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115	PHASE4	UNKNOWN	Double-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT00211796	PHASE4	COMPLETED	Divalproex Sodium ER in Adult Autism
NCT00391261	PHASE4	COMPLETED	An Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT00409747	PHASE4	COMPLETED	Minocycline to Treat Childhood Regressive Autism
NCT00576732	PHASE4	COMPLETED	A Study of the Effectiveness and Safety of Two Doses of Risperidone in the Treatment of Children and Adolescents With Autistic Disorder
NCT00844753	PHASE4	COMPLETED	Atomoxetine, Placebo and Parent Management Training in Autism
NCT01028820	PHASE4	COMPLETED	FMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01098383	PHASE4	UNKNOWN	Treatment With Acetyl-Choline Esterase Inhibitors in Children With Autism Spectrum Disorders
NCT01333865	PHASE4	COMPLETED	A Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700	PHASE4	COMPLETED	Milnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200	PHASE4	COMPLETED	Omega-3 Fatty Acids in Autism Spectrum Disorders
NCT02069977	PHASE4	UNKNOWN	Study to Evaluate the Efficacy and Safety of Aripiprazole
NCT02096952	PHASE4	COMPLETED	Methylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02199925	PHASE4	UNKNOWN	An Open-Label Study to Evaluate the Efficacy of High-Dose Gammaplex in Children on the Autism Spectrum
NCT02235467	PHASE4	COMPLETED	Multisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02255565	PHASE4	COMPLETED	Dose Response Effects of Quillivant XR in Children With ADHD and Autism: A Pilot Study
NCT02940574	PHASE4	COMPLETED	Neural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629	PHASE4	COMPLETED	Promoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646	PHASE4	COMPLETED	Evaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431	PHASE4	COMPLETED	Improving Driving in Young People With Autism Spectrum Disorders
NCT03757585	PHASE4	COMPLETED	Natural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353	PHASE4	COMPLETED	Pragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656	PHASE4	COMPLETED	Biomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245	PHASE4	UNKNOWN	Safety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339	PHASE4	RECRUITING	AWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052	PHASE4	TERMINATED	A Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665	PHASE4	RECRUITING	The TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697	PHASE4	COMPLETED	Pilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804	PHASE4	COMPLETED	Pilot RCT Using Homeopathic Medicines in ASD
NCT07439042	PHASE4	NOT_YET_RECRUITING	Buspirone for Anxiety in Autistic Youth
NCT02559102	PHASE3	COMPLETED	Dexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079	PHASE3	COMPLETED	Study of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480	PHASE3	RECRUITING	Reducing Missed Appointments
NCT07377032	PHASE3	RECRUITING	TAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT03414970	PHASE3	ACTIVE_NOT_RECRUITING	Hypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00036231	PHASE3	TERMINATED	Synthetic Human Secretin in Children With Autism and Gastrointestinal Dysfunction
NCT00036244	PHASE3	COMPLETED	Synthetic Human Secretin in Children With Autism
NCT00065884	PHASE3	UNKNOWN	Valproate Response in Aggressive Autistic Adolescents
NCT00065962	PHASE3	COMPLETED	Secretin for the Treatment of Autism