DDX47

Summary

DDX47 (DEAD-box helicase 47, HGNC:18682) is a protein-coding gene on chromosome 12p13.1, encoding Probable ATP-dependent RNA helicase DDX47 (Q9H0S4). Required for efficient ribosome biogenesis. It is a common-essential gene (DepMap: required in 100.0% of cancer cell lines).

This gene encodes a member of the DEAD box protein family. DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure, such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The protein encoded by this gene can shuttle between the nucleus and the cytoplasm, and has an RNA-independent ATPase activity. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.

Source: NCBI Gene 51202 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 105 total
• Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_016355

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18682
Approved symbol	DDX47
Name	DEAD-box helicase 47
Location	12p13.1
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp564O176, FLJ30012, HQ0256, RRP3
Ensembl gene	ENSG00000213782
Ensembl biotype	protein_coding
OMIM	615428
Entrez	51202

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 7 protein_coding, 7 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000352940, ENST00000358007, ENST00000392155, ENST00000426619, ENST00000535722, ENST00000541537, ENST00000542123, ENST00000542832, ENST00000544032, ENST00000544400, ENST00000544497, ENST00000545038, ENST00000854248, ENST00000854249, ENST00000946641, ENST00000946642

RefSeq mRNA: 2 — MANE Select: NM_016355 NM_016355, NM_201224

CCDS: CCDS8655, CCDS8656

Canonical transcript exons

ENST00000358007 — 12 exons

Exon	Start	End
ENSE00003467199	12823870	12824016
ENSE00003467946	12821208	12821396
ENSE00003476745	12823203	12823319
ENSE00003490220	12821965	12822083
ENSE00003497334	12821655	12821726
ENSE00003591338	12813346	12813454
ENSE00003598448	12829423	12829981
ENSE00003629044	12826000	12826070
ENSE00003665143	12814131	12814224
ENSE00003671579	12827246	12827375
ENSE00003683557	12822661	12822732
ENSE00003684379	12824540	12824677

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 94.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.2429 / max 66.4794, expressed in 1318 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
124363	49.7166	1815
124365	1.6748	906
124364	1.3735	786
124368	0.1078	24
124367	0.0867	37

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
islet of Langerhans	UBERON:0000006	94.99	gold quality
ventricular zone	UBERON:0003053	94.82	gold quality
smooth muscle tissue	UBERON:0001135	94.79	gold quality
skin of abdomen	UBERON:0001416	94.44	gold quality
zone of skin	UBERON:0000014	94.12	gold quality
body of uterus	UBERON:0009853	94.05	gold quality
body of pancreas	UBERON:0001150	93.93	gold quality
pancreas	UBERON:0001264	93.92	gold quality
skin of leg	UBERON:0001511	93.92	gold quality
left lobe of thyroid gland	UBERON:0001120	93.87	gold quality
thyroid gland	UBERON:0002046	93.76	gold quality
left ovary	UBERON:0002119	93.75	gold quality
ovary	UBERON:0000992	93.59	gold quality
myometrium	UBERON:0001296	93.59	gold quality
omental fat pad	UBERON:0010414	93.59	gold quality
thoracic mammary gland	UBERON:0005200	93.57	gold quality
fallopian tube	UBERON:0003889	93.53	gold quality
lower esophagus muscularis layer	UBERON:0035833	93.41	gold quality
lower esophagus	UBERON:0013473	93.39	gold quality
ectocervix	UBERON:0012249	93.37	gold quality
adipose tissue	UBERON:0001013	93.36	gold quality
rectum	UBERON:0001052	93.36	gold quality
lymph node	UBERON:0000029	93.32	gold quality
left uterine tube	UBERON:0001303	93.31	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	93.28	gold quality
muscle layer of sigmoid colon	UBERON:0035805	93.27	gold quality
vagina	UBERON:0000996	93.26	gold quality
subcutaneous adipose tissue	UBERON:0002190	93.24	gold quality
ganglionic eminence	UBERON:0004023	93.23	gold quality
right lobe of thyroid gland	UBERON:0001119	93.20	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

39 targeting DDX47, 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-5692A	100.00	74.40	6850
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-132-3P	99.73	70.56	1424
HSA-MIR-212-3P	99.73	70.65	1424
HSA-MIR-17-3P	99.55	66.77	1311
HSA-MIR-103A-1-5P	99.39	67.78	1545
HSA-MIR-103A-2-5P	99.39	67.72	1577
HSA-MIR-513A-3P	99.39	70.63	3620
HSA-MIR-513C-3P	99.39	70.63	3620
HSA-MIR-130A-5P	99.33	70.26	2623
HSA-MIR-1912-3P	99.32	67.40	936
HSA-MIR-3606-3P	99.11	69.84	3254
HSA-MIR-1295B-5P	99.03	67.50	810
HSA-MIR-922	99.02	67.23	1838
HSA-MIR-5701	98.97	69.54	1502

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 3)

• GABARAP and DDX 47 are involved in the apoptotic process (PMID:15977068)
• DDX47, MeCP2, and other functionally heterogeneous factors protect cells from harmful R loops. (PMID:36827184)
• BIOINFORMATICS APPLICATIONS UNDER CONDITION CONTROL: HIGH DIAGNOSTIC VALUE OF DDX47 IN REAL MEDICAL SETTINGS. (PMID:37553903)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ddx47	ENSDARG00000102353
mus_musculus	Ddx47	ENSMUSG00000030204
rattus_norvegicus	Ddx47	ENSRNOG00000007838
drosophila_melanogaster	pths	FBGN0032919
caenorhabditis_elegans		WBGENE00012059

Paralogs (38): DDX20 (ENSG00000064703), DDX3Y (ENSG00000067048), DDX1 (ENSG00000079785), DDX43 (ENSG00000080007), DDX18 (ENSG00000088205), DDX24 (ENSG00000089737), DDX17 (ENSG00000100201), DDX49 (ENSG00000105671), DDX50 (ENSG00000107625), DDX5 (ENSG00000108654), DDX25 (ENSG00000109832), DDX6 (ENSG00000110367), DDX55 (ENSG00000111364), DDX59 (ENSG00000118197), DDX54 (ENSG00000123064), DDX39A (ENSG00000123136), DDX27 (ENSG00000124228), DDX31 (ENSG00000125485), DDX56 (ENSG00000136271), EIF4A3 (ENSG00000141543), DDX46 (ENSG00000145833), DDX4 (ENSG00000152670), EIF4A2 (ENSG00000156976), DDX19B (ENSG00000157349), EIF4A1 (ENSG00000161960), DDX21 (ENSG00000165732), DDX19A (ENSG00000168872), TDRD12 (ENSG00000173809), DDX23 (ENSG00000174243), DDX10 (ENSG00000178105), DDX28 (ENSG00000182810), DDX41 (ENSG00000183258), DDX53 (ENSG00000184735), DDX51 (ENSG00000185163), DDX42 (ENSG00000198231), DDX39B (ENSG00000198563), DDX3X (ENSG00000215301), DDX52 (ENSG00000278053)

Protein

Protein identifiers

Probable ATP-dependent RNA helicase DDX47 — Q9H0S4 (reviewed: Q9H0S4)

Alternative names: DEAD box protein 47

All UniProt accessions (2): Q9H0S4, F5H1N9

UniProt curated annotations — full annotation on UniProt →

Function. Required for efficient ribosome biogenesis. May have a role in mRNA splicing. Involved in apoptosis.

Subunit / interactions. Interacts with AGO1 and AGO2. Interacts with GABARAP. Interacts with NOL8; the interaction is RNA-dependent.

Subcellular location. Nucleus. Nucleolus.

Tissue specificity. Expressed in skin, lung and breast. Also expressed in the brain.

Similarity. Belongs to the DEAD box helicase family. DDX47/RRP3 subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9H0S4-1	1	yes
Q9H0S4-2	2

RefSeq proteins (2): NP_057439, NP_957518 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000629	RNA-helicase_DEAD-box_CS	Conserved_site
IPR001650	Helicase_C-like	Domain
IPR011545	DEAD/DEAH_box_helicase_dom	Domain
IPR014001	Helicase_ATP-bd	Domain
IPR014014	RNA_helicase_DEAD_Q_motif	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR044765	DDX47/Rrp3_DEADc	Domain
IPR050079	DEAD_box_RNA_helicase	Family

Pfam: PF00270, PF00271

Catalyzed reactions (Rhea), 1 shown:

• ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)

UniProt features (38 total): helix 12, strand 7, modified residue 4, sequence variant 2, domain 2, region of interest 2, short sequence motif 2, compositionally biased region 2, initiator methionine 1, chain 1, binding site 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
3BER	X-RAY DIFFRACTION	1.4

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H0S4-F1	85.98	0.66

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (1): 68–75

Post-translational modifications (4): 2, 9, 149, 424

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-6790901	rRNA modification in the nucleus and cytosol
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol

MSigDB gene sets: 127 (showing top): GOBP_RIBOSOME_BIOGENESIS, TSENG_IRS1_TARGETS_UP, GOBP_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, CEBPB_01, GOBP_APOPTOTIC_SIGNALING_PATHWAY, KORKOLA_EMBRYONAL_CARCINOMA_UP, GOBP_RNA_SPLICING, GOBP_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_VIA_DEATH_DOMAIN_RECEPTORS, DODD_NASOPHARYNGEAL_CARCINOMA_UP, GNF2_ELAC2, GCM_NF2, LEE_AGING_CEREBELLUM_DN, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, CETS1P54_01, REACTOME_METABOLISM_OF_RNA

GO Biological Process (6): rRNA processing (GO:0006364), mRNA processing (GO:0006397), RNA splicing (GO:0008380), extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625), apoptotic process (GO:0006915), ribosome biogenesis (GO:0042254)

GO Molecular Function (9): RNA binding (GO:0003723), RNA helicase activity (GO:0003724), ATP binding (GO:0005524), ATP hydrolysis activity (GO:0016887), nucleotide binding (GO:0000166), nucleic acid binding (GO:0003676), helicase activity (GO:0004386), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
rRNA processing in the nucleus and cytosol	2

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	3
ATP-dependent activity	2
binding	2
nuclear lumen	2
cellular anatomical structure	2
rRNA metabolic process	1
ribosome biogenesis	1
mRNA metabolic process	1
extrinsic apoptotic signaling pathway	1
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
ribonucleoprotein complex biogenesis	1
nucleic acid binding	1
helicase activity	1
ATP-dependent activity, acting on RNA	1
catalytic activity, acting on RNA	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
ribonucleoside triphosphate phosphatase activity	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
nucleic acid conformation isomerase activity	1
catalytic activity, acting on a nucleic acid	1
catalytic activity	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

3839 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DDX47	FANCD2	Q9BXW9	760
DDX47	DHX15	O43143	647
DDX47	DHX37	Q8IY37	642
DDX47	DHX8	Q14562	627
DDX47	RRP9	O43818	502
DDX47	MTREX	P42285	475
DDX47	DHX36	Q9H2U1	469
DDX47	KRR1	Q13601	466
DDX47	DDX11	Q96FC9	457
DDX47	PDCD11	Q14690	452
DDX47	RRP8	O43159	450
DDX47	NOL8	Q76FK4	445
DDX47	NOB1	Q9ULX3	444
DDX47	GABARAP	O95166	436
DDX47	DHX33	Q9H6R0	433

IntAct

116 interactions, top by confidence:

A	B	Type	Score
CEP290	CCP110	psi-mi:“MI:2364”(proximity)	0.890
SART3	PRPF4	psi-mi:“MI:0914”(association)	0.730
N	HNRNPR	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
ARIH1	SPOP	psi-mi:“MI:0914”(association)	0.530
PARVA	CCNB1	psi-mi:“MI:0914”(association)	0.530
ABT1	ZNF316	psi-mi:“MI:0914”(association)	0.530
NOL10	DDX10	psi-mi:“MI:0914”(association)	0.530
GABARAP	DDX47	psi-mi:“MI:0915”(physical association)	0.510
DDX47	GABARAP	psi-mi:“MI:0915”(physical association)	0.510
DDX21	MED19	psi-mi:“MI:2364”(proximity)	0.480
SRPK1	DDX47	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
DDX47	MLH1	psi-mi:“MI:0915”(physical association)	0.370
KRAS	DDX47	psi-mi:“MI:0915”(physical association)	0.370
Rpl35	RPS6	psi-mi:“MI:0914”(association)	0.350
Eif3a	RPSA	psi-mi:“MI:0914”(association)	0.350
RPL10	RPS6	psi-mi:“MI:0914”(association)	0.350
Srp72		psi-mi:“MI:0914”(association)	0.350
Rrbp1	PIPSL	psi-mi:“MI:0914”(association)	0.350
HNRNPU		psi-mi:“MI:0914”(association)	0.350
NPM1	RPSA	psi-mi:“MI:0914”(association)	0.350
Eif3i	CBX4	psi-mi:“MI:0914”(association)	0.350
JUN		psi-mi:“MI:0914”(association)	0.350
JUN	TPM3	psi-mi:“MI:0914”(association)	0.350
DDX41	DDX39A	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
HSCB	RBP5	psi-mi:“MI:0914”(association)	0.350
RRP1B	YY2	psi-mi:“MI:0914”(association)	0.350

BioGRID (235): DDX47 (Affinity Capture-MS), DDX47 (Affinity Capture-MS), DDX47 (Affinity Capture-MS), DDX47 (Affinity Capture-MS), DDX47 (Affinity Capture-MS), DDX47 (Affinity Capture-MS), DDX47 (Affinity Capture-MS), DDX47 (Affinity Capture-MS), CDC5L (Co-fractionation), DCAF13 (Co-fractionation), DDX47 (Co-fractionation), DDX47 (Co-fractionation), DDX47 (Co-fractionation), DDX47 (Co-fractionation), DDX47 (Co-fractionation)

ESM2 similar proteins: A1CJ18, A1D8G1, A2QY39, A3LS22, A3LWX3, A4R715, A5DIP0, A6RY31, A6ZXG9, A7TGU7, A7TJT7, A7TLA0, P23128, P26196, P39517, P54823, P54824, Q07478, Q09181, Q0CBE1, Q0IHV9, Q0U7S9, Q109G2, Q1E5R1, Q2U5A2, Q4HW67, Q4WWD3, Q54E49, Q5AAW3, Q5RFQ5, Q5ZKB9, Q6BJX6, Q6C0X2, Q6CDS6, Q6CSZ7, Q6CT49, Q6CT85, Q6FL17, Q6FQU5, Q6H7S2

Diamond homologs: A0R8U6, A1A4H6, A1CNV8, A1CR32, A1D1R8, A1D405, A2QAX7, A2RB17, A2XKG2, A3LS22, A3LSN3, A4QYM6, A4RGD1, A5DAC8, A5DKW3, A5DQF1, A5DY34, A5E2Z9, A6QRQ7, A6RUH2, A6RW56, A6ZSX1, A7A0P8, A7EML8, A7F4L5, A7TJM9, A7TS37, B9XXL6, O25029, P0C2N7, P0C2N8, P0CQ92, P0CQ93, P0CR00, P0CR01, P25888, P32892, P34580, P38712, P96614

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 152 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 events stimulated by ALK signaling in cancer	5	16.6×	2e-03
Signaling by ALK in cancer	5	13.9×	2e-03
Formation of the ternary complex, and subsequently, the 43S complex	6	13.2×	2e-03
Signaling by ALK fusions and activated point mutants	8	12.3×	2e-04
Translation initiation complex formation	6	11.7×	2e-03
Ribosomal scanning and start codon recognition	6	11.7×	2e-03
Influenza Viral RNA Transcription and Replication	5	11.0×	5e-03
Influenza Infection	5	9.0×	8e-03

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	7	9.9×	2e-03
rRNA processing	8	8.7×	2e-03
mRNA splicing, via spliceosome	10	7.0×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	83
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1310 predictions. Top by Δscore:

Variant	Effect	Δscore
12:12813428:G:GT	donor_gain	1.0000
12:12813432:A:T	donor_gain	1.0000
12:12813452:CTGGT:C	donor_loss	1.0000
12:12813453:TGG:T	donor_loss	1.0000
12:12813454:GGT:G	donor_loss	1.0000
12:12813455:G:GG	donor_gain	1.0000
12:12813455:G:T	donor_loss	1.0000
12:12813456:T:G	donor_loss	1.0000
12:12814128:A:AG	acceptor_gain	1.0000
12:12814128:AAGG:A	acceptor_gain	1.0000
12:12814129:A:G	acceptor_gain	1.0000
12:12814130:GGGT:G	acceptor_gain	1.0000
12:12814224:GGTA:G	donor_loss	1.0000
12:12821204:TTAG:T	acceptor_loss	1.0000
12:12821207:G:GT	acceptor_loss	1.0000
12:12821392:GAGTG:G	donor_gain	1.0000
12:12821393:AGTGG:A	donor_loss	1.0000
12:12821394:GTG:G	donor_gain	1.0000
12:12821394:GTGGT:G	donor_loss	1.0000
12:12821395:TGGTA:T	donor_loss	1.0000
12:12821396:GGTAA:G	donor_loss	1.0000
12:12821397:G:C	donor_loss	1.0000
12:12821398:T:A	donor_loss	1.0000
12:12821950:A:AG	acceptor_gain	1.0000
12:12821951:A:AG	acceptor_gain	1.0000
12:12821952:C:G	acceptor_gain	1.0000
12:12821959:T:TA	acceptor_gain	1.0000
12:12821960:G:A	acceptor_gain	1.0000
12:12821960:GGTA:G	acceptor_loss	1.0000
12:12821961:GTAGC:G	acceptor_loss	1.0000

AlphaMissense

2966 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:12821237:G:C	G71R	1.000
12:12821238:G:A	G71D	1.000
12:12821240:T:C	S72P	1.000
12:12821244:G:A	G73E	1.000
12:12821244:G:T	G73V	1.000
12:12821246:A:C	K74Q	1.000
12:12821247:A:T	K74M	1.000
12:12821248:G:C	K74N	1.000
12:12821248:G:T	K74N	1.000
12:12821331:G:C	R102P	1.000
12:12821333:G:A	E103K	1.000
12:12821337:T:A	L104Q	1.000
12:12821337:T:C	L104P	1.000
12:12821347:G:C	Q107H	1.000
12:12821347:G:T	Q107H	1.000
12:12821666:G:C	G128R	1.000
12:12821667:G:A	G128D	1.000
12:12821965:C:A	A148E	1.000
12:12821974:G:A	G151D	1.000
12:12821977:G:C	R152P	1.000
12:12821980:T:C	L153P	1.000
12:12822042:G:C	D174H	1.000
12:12822043:A:C	D174A	1.000
12:12822044:T:A	D174E	1.000
12:12822044:T:G	D174E	1.000
12:12822045:G:A	E175K	1.000
12:12822045:G:C	E175Q	1.000
12:12822046:A:C	E175A	1.000
12:12822046:A:G	E175G	1.000
12:12822046:A:T	E175V	1.000

dbSNP variants (sampled 300 via entrez): RS1000047404 (12:12816800 A>G,T), RS1000113015 (12:12817995 C>A,G,T), RS1000265932 (12:12824341 C>A,G), RS1000433365 (12:12817055 A>G), RS1000459133 (12:12828881 A>G), RS1000494904 (12:12819345 G>A), RS1000556607 (12:12821812 A>C), RS1000700016 (12:12824659 C>G), RS1000705177 (12:12813562 C>T), RS1000728387 (12:12819694 C>A), RS1000765526 (12:12828051 G>T), RS1000776149 (12:12812265 G>A), RS1001005329 (12:12825626 G>C), RS1001121300 (12:12816739 A>C,G), RS1001199320 (12:12827828 A>C)

Disease associations

OMIM: gene MIM:615428 | disease phenotypes: MIM:613970, MIM:616139

GenCC curated gene-disease

Mondo (3): intellectual disability, autosomal dominant 6 (MONDO:0013509), developmental and epileptic encephalopathy, 27 (MONDO:0014505), intellectual disability (MONDO:0001071)

Orphanet (3): West syndrome (Orphanet:3451), GRIN2B-related developmental delay, intellectual disability and autism spectrum disorder (Orphanet:589547), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

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

GWAS associations

0 associations (top):

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)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, decreases methylation	3
sodium arsenite	decreases expression, increases abundance	3
Smoke	increases abundance, decreases expression	2
Valproic Acid	affects expression, decreases methylation	2
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
beauvericin	affects cotreatment, increases expression	1
beta-lapachone	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
cylindrospermopsin	increases expression	1
enniatins	increases expression, affects cotreatment	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
LDN 193189	affects cotreatment, decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Caffeine	decreases phosphorylation	1
Coal	decreases expression, increases abundance	1
Gallic Acid	decreases expression	1
Hydrogen Peroxide	affects expression	1
Ivermectin	decreases expression	1
Ribonucleotides	affects binding	1
Cyclosporine	increases expression	1
Aflatoxin B1	increases expression	1
Sodium Selenite	increases expression	1
Copper Sulfate	increases expression	1
Vitamin K 3	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