TRAPPC10

Summary

TRAPPC10 (trafficking protein particle complex subunit 10, HGNC:11868) is a protein-coding gene on chromosome 21q22.3, encoding Trafficking protein particle complex subunit 10 (P48553). Specific subunit of the TRAPP (transport protein particle) II complex, a highly conserved vesicle tethering complex that functions in late Golgi trafficking as a membrane tether.

The protein encoded by this gene is a transmembrane protein found in the cis-Golgi complex. The encoded protein is part of the multisubunit transport protein particle (TRAPP) complex and may be involved in vesicular transport from the endoplasmic reticulum to the Golgi. Mutations in this gene could be responsible for the Unverricht-Lundborg type of progressive myoclonus epilepsy, or for autoimmune polyglandular disease type 1.

Source: NCBI Gene 7109 — RefSeq curated summary.

At a glance

• Gene–disease (curated): neurodevelopmental disorder with microcephaly, short stature, and speech delay (Strong, GenCC)
• GWAS associations: 6
• Clinical variants (ClinVar): 202 total — 1 pathogenic, 4 likely-pathogenic
• Phenotypes (HPO): 28
• Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
• MANE Select transcript: NM_003274

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11868
Approved symbol	TRAPPC10
Name	trafficking protein particle complex subunit 10
Location	21q22.3
Locus type	gene with protein product
Status	Approved
Aliases	EHOC-1, TRS130
Ensembl gene	ENSG00000160218
Ensembl biotype	protein_coding
OMIM	602103
Entrez	7109

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 11 protein_coding, 6 retained_intron, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000291574, ENST00000380221, ENST00000422875, ENST00000459741, ENST00000461889, ENST00000465905, ENST00000468864, ENST00000469521, ENST00000481460, ENST00000483973, ENST00000485621, ENST00000486746, ENST00000887574, ENST00000887575, ENST00000887576, ENST00000915072, ENST00000915073, ENST00000915074, ENST00000915075, ENST00000915076, ENST00000915077

RefSeq mRNA: 2 — MANE Select: NM_003274 NM_001351709, NM_003274

CCDS: CCDS13704

Canonical transcript exons

ENST00000291574 — 23 exons

Exon	Start	End
ENSE00001050653	44059103	44059214
ENSE00001050656	44055698	44055893
ENSE00001050659	44052280	44052476
ENSE00002279965	44037792	44037927
ENSE00002296925	44032091	44032172
ENSE00003467272	44082788	44083302
ENSE00003483630	44103293	44106552
ENSE00003535430	44074324	44074470
ENSE00003554204	44079564	44079704
ENSE00003571790	44086802	44086960
ENSE00003577489	44063538	44063785
ENSE00003580944	44102778	44102972
ENSE00003603102	44098357	44098534
ENSE00003612209	44089833	44089933
ENSE00003620582	44094063	44094233
ENSE00003627568	44087699	44087928
ENSE00003630584	44091923	44092049
ENSE00003640080	44080015	44080127
ENSE00003647654	44084122	44084263
ENSE00003655278	44076552	44076628
ENSE00003677669	44077693	44077784
ENSE00003689258	44075039	44075153
ENSE00003843183	44012309	44012560

Expression profiles

Bgee: expression breadth ubiquitous, 195 present calls, max score 94.05.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 47.0020 / max 2736.9650, expressed in 1823 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
189418	46.3186	1823
189417	0.2351	89
189423	0.2326	79
189420	0.1647	76
189422	0.0509	22

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bone marrow cell	CL:0002092	94.05	gold quality
granulocyte	CL:0000094	91.21	gold quality
rectum	UBERON:0001052	90.66	gold quality
vermiform appendix	UBERON:0001154	90.36	gold quality
leukocyte	CL:0000738	90.23	gold quality
monocyte	CL:0000576	89.87	gold quality
stromal cell of endometrium	CL:0002255	89.39	gold quality
cortical plate	UBERON:0005343	88.93	gold quality
colonic epithelium	UBERON:0000397	88.59	gold quality
transverse colon	UBERON:0001157	88.57	gold quality
small intestine Peyer’s patch	UBERON:0003454	88.56	gold quality
sural nerve	UBERON:0015488	88.30	gold quality
islet of Langerhans	UBERON:0000006	87.71	gold quality
metanephros cortex	UBERON:0010533	87.70	gold quality
lymph node	UBERON:0000029	87.37	gold quality
right lobe of thyroid gland	UBERON:0001119	86.81	gold quality
upper lobe of left lung	UBERON:0008952	86.61	gold quality
right uterine tube	UBERON:0001302	86.25	gold quality
spleen	UBERON:0002106	86.21	gold quality
left lobe of thyroid gland	UBERON:0001120	86.19	gold quality
right lung	UBERON:0002167	86.04	gold quality
gastrocnemius	UBERON:0001388	86.00	gold quality
small intestine	UBERON:0002108	85.96	gold quality
prefrontal cortex	UBERON:0000451	85.91	gold quality
smooth muscle tissue	UBERON:0001135	85.79	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	85.78	gold quality
nerve	UBERON:0001021	85.54	gold quality
tibial nerve	UBERON:0001323	85.54	gold quality
muscle of leg	UBERON:0001383	85.54	gold quality
gall bladder	UBERON:0002110	85.47	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.26
E-MTAB-7303	no	184.72

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

140 targeting TRAPPC10, 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-4673	100.00	66.64	1490
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-5692A	100.00	74.40	6850
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-4282	99.99	75.36	6408
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-3658	99.96	73.87	4379
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-548AE-3P	99.93	72.66	4867

Functional genomics

ClinGen dosage: haploinsufficiency 0 (no evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	trappc10	ENSDARG00000098118
mus_musculus	Trappc10	ENSMUSG00000000374
rattus_norvegicus	Trappc10	ENSRNOG00000023210
drosophila_melanogaster	SIDL	FBGN0038303
caenorhabditis_elegans	trpp-10	WBGENE00022138

Protein

Protein identifiers

Trafficking protein particle complex subunit 10 — P48553 (reviewed: P48553)

Alternative names: Epilepsy holoprosencephaly candidate 1 protein, Protein GT334, Trafficking protein particle complex subunit TMEM1, Transport protein particle subunit TMEM1

All UniProt accessions (2): P48553, F8WE24

UniProt curated annotations — full annotation on UniProt →

Function. Specific subunit of the TRAPP (transport protein particle) II complex, a highly conserved vesicle tethering complex that functions in late Golgi trafficking as a membrane tether.

Subunit / interactions. Specific component of the multisubunit TRAPP II complex, which includes at least TRAPPC1, TRAPPC2, TRAPPC3, TRAPPC4, TRAPPC5, TRAPPC6A/B, TRAPPC9, TRAPPC10 and TRAPPC14. TRAPPC9, TRAPPC10 and TRAPPC14 are specific subunits of the TRAPP II complex. Interacts with TRAPPC14.

Subcellular location. Golgi apparatus. cis-Golgi network.

Tissue specificity. Expressed in all tissues examined.

Disease relevance. Neurodevelopmental disorder with microcephaly, short stature, and speech delay (NEDMISS) [MIM:620027] An autosomal recessive disorder characterized by global developmental delay, short stature, severely impaired intellectual development, microcephaly, poor or absent speech, and behavioral abnormalities including autistic features and aggressive behavior. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the TRAPPC10 family.

Isoforms (2)

UniProt ID	Names	Canonical?
P48553-1	1	yes
P48553-2	2

RefSeq proteins (2): NP_001338638, NP_003265* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR022233	TRAPPC10/Trs130_C	Domain
IPR045126	TRAPPC10/Trs130	Family
IPR056913	TRAPPC10/Trs130_N	Domain
IPR056917	Ig_TRAPPC10	Domain

Pfam: PF12584, PF23036, PF23604

UniProt features (13 total): sequence conflict 4, sequence variant 4, splice variant 2, chain 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P48553-F1	79.50	0.35

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 (1): 708

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-204005	COPII-mediated vesicle transport
R-HSA-8876198	RAB GEFs exchange GTP for GDP on RABs

MSigDB gene sets: 217 (showing top): GOBP_VESICLE_LOCALIZATION, GOBP_VESICLE_ORGANIZATION, GOBP_VESICLE_TARGETING, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, ACTGCAG_MIR173P, GOBP_INTRA_GOLGI_VESICLE_MEDIATED_TRANSPORT, GTGCCTT_MIR506, ONKEN_UVEAL_MELANOMA_UP, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, DER_IFN_BETA_RESPONSE_UP, GOBP_EARLY_ENDOSOME_TO_GOLGI_TRANSPORT, GOBP_MEMBRANE_ORGANIZATION, ZHANG_BREAST_CANCER_PROGENITORS_UP

GO Biological Process (7): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), intra-Golgi vesicle-mediated transport (GO:0006891), vesicle coat assembly (GO:0006901), early endosome to Golgi transport (GO:0034498), obsolete vesicle tethering (GO:0099022), vesicle-mediated transport (GO:0016192), Golgi vesicle transport (GO:0048193)

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

GO Cellular Component (5): cytoplasm (GO:0005737), cytosol (GO:0005829), TRAPP complex (GO:0030008), TRAPPII protein complex (GO:1990071), Golgi apparatus (GO:0005794)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
ER to Golgi Anterograde Transport	1
Rab regulation of trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	3
Golgi vesicle transport	3
cellular anatomical structure	2
intercellular transport	1
intracellular transport	1
vesicle budding from membrane	1
vesicle organization	1
retrograde transport, endosome to Golgi	1
transport	1
cellular process	1
vesicle-mediated transport	1
binding	1
intracellular anatomical structure	1
vesicle tethering complex	1
intracellular protein-containing complex	1
endosome	1
Golgi apparatus	1
TRAPP complex	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

944 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRAPPC10	TRAPPC9	Q96Q05	997
TRAPPC10	TRAPPC8	Q9Y2L5	947
TRAPPC10	PWP2	Q15269	924
TRAPPC10	TRAPPC2	P0DI81	921
TRAPPC10	TRAPPC4	Q9Y296	913
TRAPPC10	LETM1	O95202	905
TRAPPC10	TRAPPC3	O43617	887
TRAPPC10	TRAPPC6A	O75865	882
TRAPPC10	TRAPPC5	Q8IUR0	882
TRAPPC10	LRRTM1	Q86UE6	865
TRAPPC10	TRAPPC13	A5PLN9	858
TRAPPC10	TRAPPC1	Q9Y5R8	838
TRAPPC10	TRAPPC12	Q8WVT3	824
TRAPPC10	TRAPPC2L	Q9UL33	803
TRAPPC10	TRAPPC6B	Q86SZ2	793

IntAct

107 interactions, top by confidence:

A	B	Type	Score
RUFY4	NDC80	psi-mi:“MI:0914”(association)	0.830
RAB3IP	TRAPPC10	psi-mi:“MI:0915”(physical association)	0.770
TRAPPC10	RAB3IP	psi-mi:“MI:0403”(colocalization)	0.770
SART1	PRPF6	psi-mi:“MI:0914”(association)	0.750
SART1	PRPF3	psi-mi:“MI:0914”(association)	0.720
RAB3IP	TRAPPC3	psi-mi:“MI:0914”(association)	0.700
RAB3IP	TRAPPC3	psi-mi:“MI:0915”(physical association)	0.700
PTGR3	DBT	psi-mi:“MI:0914”(association)	0.640
KANK4	TRAPPC3	psi-mi:“MI:0914”(association)	0.640
KANK4	TRAPPC10	psi-mi:“MI:0914”(association)	0.640
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
APBA1	LIN7A	psi-mi:“MI:0914”(association)	0.590
TRAPPC2L	TRAPPC13	psi-mi:“MI:0914”(association)	0.560
RAB3IP	TRAPPC2	psi-mi:“MI:0914”(association)	0.560
RAB30	UBB	psi-mi:“MI:0914”(association)	0.530
BTBD1	TRAPPC10	psi-mi:“MI:0914”(association)	0.530
TRAPPC1	TRAPPC13	psi-mi:“MI:0914”(association)	0.530
BCL2L14	CHEK1	psi-mi:“MI:0914”(association)	0.530
CABS1	TRAPPC10	psi-mi:“MI:0914”(association)	0.530
SLC31A1	C2orf72	psi-mi:“MI:0914”(association)	0.530

BioGRID (133): GPD2 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), GPD2 (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IES7, A0JN62, A0JNW5, A2AAE1, A2AGL3, A2RSJ4, A2RT67, A2RUS2, A2RV80, B0LPN4, B1H2P5, E7F240, E9Q401, O00507, O94967, P30957, P48553, P51593, Q14161, Q2LD37, Q3TLI0, Q3UHE1, Q3UVG3, Q3UX43, Q5F361, Q5M7Q1, Q5RAQ5, Q5ZJK1, Q658Y4, Q68CL5, Q6BDS2, Q6P6Y1, Q6TEP1, Q6VNB8, Q7TMY8, Q7TSG1, Q7Z6Z7, Q8BHY8, Q8CB44, Q8CGF6

Diamond homologs: P48553, Q3TLI0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 100 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
RAB GEFs exchange GTP for GDP on RABs	11	19.5×	5e-09
COPII-mediated vesicle transport	8	18.6×	3e-06
Translocation of SLC2A4 (GLUT4) to the plasma membrane	6	13.2×	5e-04
Membrane Trafficking	9	4.8×	6e-03
Vesicle-mediated transport	9	4.5×	9e-03

GO biological processes:

GO term	Partners	Fold	FDR
obsolete vesicle tethering	8	90.1×	4e-12
COPII vesicle coat assembly	6	47.9×	4e-07
endoplasmic reticulum to Golgi vesicle-mediated transport	10	15.4×	3e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	4
Uncertain significance	149
Likely benign	18
Benign	1

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
1704295	NM_003274.5(TRAPPC10):c.3392del (p.Gly1131fs)	Pathogenic
1691454	NM_003274.5(TRAPPC10):c.3222C>A (p.Cys1074Ter)	Likely pathogenic
2502438	NM_003274.5(TRAPPC10):c.1512_1513insAA (p.Ala505fs)	Likely pathogenic
2502439	NM_003274.5(TRAPPC10):c.940C>T (p.Gln314Ter)	Likely pathogenic
3600370	NM_003274.5(TRAPPC10):c.1300+1G>A	Likely pathogenic

SpliceAI

4750 predictions. Top by Δscore:

Variant	Effect	Δscore
21:44012558:CCT:C	donor_gain	1.0000
21:44012559:CT:C	donor_gain	1.0000
21:44012560:TGTG:T	donor_loss	1.0000
21:44012561:G:GG	donor_gain	1.0000
21:44012561:GT:G	donor_loss	1.0000
21:44032085:TCATA:T	acceptor_loss	1.0000
21:44032086:CATA:C	acceptor_loss	1.0000
21:44032087:ATAGG:A	acceptor_loss	1.0000
21:44032088:TA:T	acceptor_loss	1.0000
21:44032089:A:AG	acceptor_gain	1.0000
21:44032089:A:AT	acceptor_loss	1.0000
21:44032090:G:A	acceptor_loss	1.0000
21:44032090:G:GG	acceptor_gain	1.0000
21:44032090:GGT:G	acceptor_gain	1.0000
21:44032169:GAAG:G	donor_gain	1.0000
21:44032173:G:A	donor_loss	1.0000
21:44037926:GT:G	donor_gain	1.0000
21:44052274:TTTTA:T	acceptor_loss	1.0000
21:44052275:TTTAG:T	acceptor_loss	1.0000
21:44052276:TTA:T	acceptor_loss	1.0000
21:44052278:AGGAT:A	acceptor_loss	1.0000
21:44052279:G:GT	acceptor_loss	1.0000
21:44059079:A:AG	acceptor_gain	1.0000
21:44059080:A:AG	acceptor_gain	1.0000
21:44059081:A:G	acceptor_gain	1.0000
21:44059081:AAAAC:A	acceptor_gain	1.0000
21:44059082:A:AG	acceptor_gain	1.0000
21:44059083:A:AG	acceptor_gain	1.0000
21:44059085:C:CA	acceptor_gain	1.0000
21:44059092:T:A	acceptor_gain	1.0000

AlphaMissense

8306 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
21:44012555:T:A	V21D	1.000
21:44032165:T:A	W48R	1.000
21:44032165:T:C	W48R	1.000
21:44032167:G:C	W48C	1.000
21:44032167:G:T	W48C	1.000
21:44032172:G:T	R50M	1.000
21:44052325:T:A	W111R	1.000
21:44052325:T:C	W111R	1.000
21:44055832:G:C	R206T	1.000
21:44055833:A:C	R206S	1.000
21:44055833:A:T	R206S	1.000
21:44055841:G:T	R209M	1.000
21:44055864:T:A	W217R	1.000
21:44055864:T:C	W217R	1.000
21:44059110:T:C	L229P	1.000
21:44059113:C:A	A230D	1.000
21:44059131:T:C	L236P	1.000
21:44059148:G:C	A242P	1.000
21:44059149:C:A	A242D	1.000
21:44059152:T:C	L243P	1.000
21:44059170:T:C	L249P	1.000
21:44059179:T:C	L252P	1.000
21:44102798:T:A	W1123R	1.000
21:44102798:T:C	W1123R	1.000
21:44012549:C:A	P19H	0.999
21:44032166:G:C	W48S	0.999
21:44032172:G:C	R50T	0.999
21:44037792:G:C	R50S	0.999
21:44037792:G:T	R50S	0.999
21:44037902:T:C	L87P	0.999

dbSNP variants (sampled 300 via entrez): RS1000056650 (21:44042748 G>C), RS1000087313 (21:44030253 G>A,C), RS1000108698 (21:44043160 T>C), RS1000136016 (21:44054864 G>A), RS1000181401 (21:44016866 G>A,T), RS1000185684 (21:44083759 C>T), RS1000186777 (21:44045763 G>A), RS1000195163 (21:44097330 C>T), RS1000224188 (21:44089737 G>A,T), RS1000244480 (21:44012375 G>A,C), RS1000255526 (21:44089511 G>A,C), RS1000287945 (21:44089221 C>T), RS1000288901 (21:44060495 T>C), RS1000294119 (21:44062909 T>C), RS1000345944 (21:44085792 C>T)

Disease associations

OMIM: gene MIM:602103 | disease phenotypes: MIM:620027

GenCC curated gene-disease

Disease	Classification	Inheritance
neurodevelopmental disorder with microcephaly, short stature, and speech delay	Strong	Autosomal recessive

Mondo (2): neurodevelopmental disorder with microcephaly, short stature, and speech delay (MONDO:0859285), intellectual disability (MONDO:0001071)

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

HPO phenotypes

28 total (28 of 28 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000076	Vesicoureteral reflux
HP:0000122	Unilateral renal agenesis
HP:0000219	Thin upper lip vermilion
HP:0000252	Microcephaly
HP:0000340	Sloping forehead
HP:0000582	Upslanted palpebral fissure
HP:0000664	Synophrys
HP:0000718	Aggressive behavior
HP:0000750	Delayed speech and language development
HP:0001250	Seizure
HP:0001252	Hypotonia
HP:0001263	Global developmental delay
HP:0001274	Agenesis of corpus callosum
HP:0001302	Pachygyria
HP:0001344	Absent speech
HP:0001347	Hyperreflexia
HP:0001510	Growth delay
HP:0002119	Ventriculomegaly
HP:0002282	Gray matter heterotopia
HP:0002465	Poor speech
HP:0002515	Waddling gait
HP:0003103	Abnormal cortical bone morphology
HP:0004322	Short stature
HP:0007333	Hypoplasia of the frontal lobes
HP:0010864	Severe intellectual disability
HP:0011463	Childhood onset
HP:0031936	Delayed ability to walk

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST009391_1236	Metabolite levels	2.000000e-06
GCST009391_1244	Metabolite levels	3.000000e-08
GCST009391_1486	Metabolite levels	9.000000e-06
GCST009391_1490	Metabolite levels	2.000000e-07
GCST009391_1515	Metabolite levels	6.000000e-06
GCST009391_1957	Metabolite levels	1.000000e-06

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0010422	triacylglycerol 54:4 measurement
EFO:0010423	triacylglycerol 54:5 measurement
EFO:0010414	triacylglycerol 52:2 measurement
EFO:0010416	triacylglycerol 52:4 measurement
EFO:0010417	triacylglycerol 52:5 measurement
EFO:0010424	triacylglycerol 54:6 measurement

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

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression, affects cotreatment, increases methylation	3
trichostatin A	affects cotreatment, increases expression	3
Acetaminophen	increases expression	2
FR900359	increases phosphorylation	1
2,4,6-tribromophenol	decreases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
decabromobiphenyl ether	increases expression	1
2-butenal	decreases expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, decreases reaction	1
sodium arsenite	increases expression	1
tetrabromobisphenol A	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
pentabrominated diphenyl ether 100	increases expression	1
hexabrominated diphenyl ether 153	increases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	decreases expression	1
Demecolcine	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects expression, increases abundance	1
Quercetin	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_XU70	HAP1 TRAPPC10 (-)	Cancer cell line	Male

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