TRAPPC2L

Summary

TRAPPC2L (trafficking protein particle complex subunit 2L, HGNC:30887) is a protein-coding gene on chromosome 16q24.3, encoding Trafficking protein particle complex subunit 2-like protein (Q9UL33). Plays a role in vesicular transport from endoplasmic reticulum to Golgi. It is a selective cancer dependency (DepMap: 15.2% of cell lines).

This gene encodes a protein that interacts with the tethering factor trafficking protein particle (TRAPP complex). TRAPP complexes mediate the contact between vescicles and target membranes, and thus, are involved in vescicle-mediated transport of proteins and lipids. The encoded protein is related to the X-linked trafficking protein particle complex 2. A related pseudogene is located on the X chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 51693 — RefSeq curated summary.

At a glance

• Gene–disease (curated): encephalopathy, progressive, early-onset, with episodic rhabdomyolysis (Strong, GenCC)
• GWAS associations: 2
• Clinical variants (ClinVar): 79 total — 4 pathogenic, 2 likely-pathogenic
• Phenotypes (HPO): 16
• Cancer dependency (DepMap): dependent in 15.2% of screened cell lines
• MANE Select transcript: NM_001318525

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30887
Approved symbol	TRAPPC2L
Name	trafficking protein particle complex subunit 2L
Location	16q24.3
Locus type	gene with protein product
Status	Approved
Aliases	HSPC176
Ensembl gene	ENSG00000167515
Ensembl biotype	protein_coding
OMIM	610970
Entrez	51693

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 16 protein_coding, 4 retained_intron, 3 nonsense_mediated_decay

ENST00000301021, ENST00000561840, ENST00000562125, ENST00000562792, ENST00000563514, ENST00000564365, ENST00000564404, ENST00000564547, ENST00000565205, ENST00000565309, ENST00000565504, ENST00000567312, ENST00000567895, ENST00000568583, ENST00000625770, ENST00000696289, ENST00000858705, ENST00000938854, ENST00000938855, ENST00000938856, ENST00000938857, ENST00000938858, ENST00000938859

RefSeq mRNA: 9 — MANE Select: NM_001318525 NM_001318524, NM_001318525, NM_001318526, NM_001318527, NM_001318528, NM_001318529, NM_001318530, NM_001318532, NM_016209

CCDS: CCDS10971, CCDS82027, CCDS82028, CCDS82029, CCDS92207

Canonical transcript exons

ENST00000696289 — 5 exons

Exon	Start	End
ENSE00001113787	88859663	88859750
ENSE00001113790	88858619	88858791
ENSE00002577015	88860914	88862678
ENSE00002603654	88857127	88857183
ENSE00003498409	88859893	88859972

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 97.96.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 47.9946 / max 205.4711, expressed in 1824 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
155560	47.9946	1824

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right adrenal gland cortex	UBERON:0035827	97.96	gold quality
right adrenal gland	UBERON:0001233	97.94	gold quality
right testis	UBERON:0004534	97.83	gold quality
left adrenal gland cortex	UBERON:0035825	97.80	gold quality
left testis	UBERON:0004533	97.79	gold quality
left adrenal gland	UBERON:0001234	97.77	gold quality
adrenal cortex	UBERON:0001235	97.41	gold quality
adrenal gland	UBERON:0002369	97.11	gold quality
prefrontal cortex	UBERON:0000451	97.01	gold quality
testis	UBERON:0000473	96.56	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	96.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	96.24	gold quality
ventricular zone	UBERON:0003053	95.99	gold quality
islet of Langerhans	UBERON:0000006	95.38	gold quality
nucleus accumbens	UBERON:0001882	95.31	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	95.24	gold quality
spinal cord	UBERON:0002240	95.23	gold quality
anterior cingulate cortex	UBERON:0009835	95.13	gold quality
adrenal tissue	UBERON:0018303	95.08	gold quality
body of stomach	UBERON:0001161	95.06	gold quality
cingulate cortex	UBERON:0003027	95.06	gold quality
apex of heart	UBERON:0002098	95.03	gold quality
amygdala	UBERON:0001876	94.81	gold quality
right frontal lobe	UBERON:0002810	94.75	gold quality
right atrium auricular region	UBERON:0006631	94.72	gold quality
mucosa of transverse colon	UBERON:0004991	94.58	gold quality
left ovary	UBERON:0002119	94.56	gold quality
ganglionic eminence	UBERON:0004023	94.51	gold quality
putamen	UBERON:0001874	94.38	gold quality
frontal cortex	UBERON:0001870	94.27	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.36
E-MTAB-6379	no	312.53

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ESR1

miRNA regulators (miRDB)

51 targeting TRAPPC2L, 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-3667-3P	99.99	67.17	1636
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-320A-3P	99.77	69.73	2107
HSA-MIR-320B	99.77	69.73	2107
HSA-MIR-320C	99.77	69.73	2107
HSA-MIR-320D	99.77	69.73	2107
HSA-MIR-4429	99.77	69.62	2111
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-18A-3P	99.56	65.68	1092
HSA-MIR-4452	99.50	68.45	1493
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-6507-3P	99.35	67.32	1059
HSA-MIR-4279	99.19	66.70	2437

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 15.2% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

• deleterious bi-allelic variants in TRAPPC2L are associated with encephalopathy and febrile illness-induced episodes of rhabdomyolysis and subsequent developmental arrest. While the exact pathophysiological route deserves further study, our results suggest a role for RAB11. (PMID:30120216)
• A novel homozygous variant in TRAPPC2L results in a neurodevelopmental disorder and disrupts TRAPP complex function. (PMID:32843486)
• TRAPPC2L-related disorder: first homozygous protein-truncating variant and further delineation of the phenotype. (PMID:36849228)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	trappc2l	ENSDARG00000111785
mus_musculus	Trappc2l	ENSMUSG00000015013
rattus_norvegicus	LOC100909916	ENSRNOG00000032666
rattus_norvegicus		ENSRNOG00000074962
drosophila_melanogaster	CG9067	FBGN0033605
caenorhabditis_elegans		WBGENE00044604

Paralogs (2): TRAPPC2 (ENSG00000196459), TRAPPC2B (ENSG00000256060)

Protein

Protein identifiers

Trafficking protein particle complex subunit 2-like protein — Q9UL33 (reviewed: Q9UL33)

All UniProt accessions (9): A0A0B4J286, A0A0B4J294, Q9UL33, H3BP13, H3BPE0, H3BPN3, H3BPS1, H3BQQ8, H3BUK6

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in vesicular transport from endoplasmic reticulum to Golgi.

Subunit / interactions. Component of the multisubunit TRAPP (transport protein particle) complex, which includes at least TRAPPC2, TRAPPC2L, TRAPPC3, TRAPPC3L, TRAPPC4, TRAPPC5, TRAPPC8, TRAPPC9, TRAPPC10, TRAPPC11 and TRAPPC12. Interacts with the heterodimer TRAPPC3-TRAPPC6A. Interacts with TRAPPC6A.

Subcellular location. Cytoplasm. Perinuclear region. Endoplasmic reticulum. Golgi apparatus.

Tissue specificity. Expressed in testis, liver, bladder, lung, spleen and brain, several cell lines and primary chondrocytes cell line.

Disease relevance. Encephalopathy, progressive, early-onset, with episodic rhabdomyolysis (PEERB) [MIM:618331] An autosomal recessive disease characterized by progressive encephalopathy exacerbated by febrile illness and associated with severe neurodevelopmental delay, episodes of rhabdomyolysis, developmental regression, epilepsy and tetraplegia. The disease may be caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the TRAPP small subunits family. Sedlin subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9UL33-1	1	yes
Q9UL33-2	2

RefSeq proteins (9): NP_001305453, NP_001305454, NP_001305455, NP_001305456, NP_001305457, NP_001305458, NP_001305459, NP_001305461, NP_057293 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006722	Sedlin	Family
IPR011012	Longin-like_dom_sf	Homologous_superfamily
IPR044760	TRAPPC2L	Family

Pfam: PF04628

UniProt features (3 total): chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UL33-F1	92.21	0.81

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: 173 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, GOBP_VESICLE_LOCALIZATION, GOBP_VESICLE_ORGANIZATION, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_VESICLE_TARGETING, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, TIEN_INTESTINE_PROBIOTICS_24HR_UP, GOBP_MEMBRANE_ORGANIZATION, GOBP_ORGANELLE_LOCALIZATION, GOBP_GOLGI_VESICLE_TRANSPORT, JIANG_VHL_TARGETS

GO Biological Process (5): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), vesicle coat assembly (GO:0006901), COPII vesicle coat assembly (GO:0048208), obsolete vesicle tethering (GO:0099022), vesicle-mediated transport (GO:0016192)

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

GO Cellular Component (9): nucleus (GO:0005634), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), cytosol (GO:0005829), TRAPP complex (GO:0030008), perinuclear region of cytoplasm (GO:0048471), TRAPPII protein complex (GO:1990071), TRAPPIII protein complex (GO:1990072), 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	5
intracellular membrane-bounded organelle	3
cellular anatomical structure	3
endomembrane system	2
Golgi apparatus	2
TRAPP complex	2
intercellular transport	1
intracellular transport	1
Golgi vesicle transport	1
vesicle budding from membrane	1
vesicle organization	1
vesicle coat assembly	1
protein-containing complex assembly	1
COPII-coated vesicle budding	1
transport	1
cellular process	1
binding	1
intracellular anatomical structure	1
vesicle tethering complex	1
intracellular protein-containing complex	1
endosome	1

Protein interactions and networks

STRING

1128 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRAPPC2L	TRAPPC12	Q8WVT3	859
TRAPPC2L	TRAPPC2	P0DI81	852
TRAPPC2L	TRAPPC8	Q9Y2L5	845
TRAPPC2L	TRAPPC13	A5PLN9	815
TRAPPC2L	TRAPPC9	Q96Q05	813
TRAPPC2L	TRAPPC11	Q7Z392	811
TRAPPC2L	TRAPPC10	P48553	803
TRAPPC2L	TRAPPC6A	O75865	725
TRAPPC2L	TRAPPC4	Q9Y296	719
TRAPPC2L	TRAPPC1	Q9Y5R8	717
TRAPPC2L	TRAPPC3	O43617	709
TRAPPC2L	TRAPPC6B	Q86SZ2	668
TRAPPC2L	TRAPPC5	Q8IUR0	667
TRAPPC2L	CD34	P28906	549
TRAPPC2L	TRAPPC3L	Q5T215	539

IntAct

77 interactions, top by confidence:

A	B	Type	Score
TRAPPC3	TRAPPC2L	psi-mi:“MI:0915”(physical association)	0.880
TRAPPC2L	TRAPPC3	psi-mi:“MI:0915”(physical association)	0.880
RUFY4	NDC80	psi-mi:“MI:0914”(association)	0.830
RAB3IP	TRAPPC3	psi-mi:“MI:0914”(association)	0.700
TRAPPC2L	REPS1	psi-mi:“MI:0915”(physical association)	0.560
TCF4	TRAPPC2L	psi-mi:“MI:0915”(physical association)	0.560
TRAPPC2L	REL	psi-mi:“MI:0915”(physical association)	0.560
TRAPPC2L	TRIP6	psi-mi:“MI:0915”(physical association)	0.560
CEP57L1	TRAPPC2L	psi-mi:“MI:0915”(physical association)	0.560
TRAPPC2L	BLZF1	psi-mi:“MI:0915”(physical association)	0.560
TRAPPC2L	TCF4	psi-mi:“MI:0915”(physical association)	0.560
TRAPPC2L	CEP57L1	psi-mi:“MI:0915”(physical association)	0.560
BLZF1	TRAPPC2L	psi-mi:“MI:0915”(physical association)	0.560
REL	TRAPPC2L	psi-mi:“MI:0915”(physical association)	0.560
REPS1	TRAPPC2L	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (182): TRAPPC2L (Two-hybrid), TRAPPC2L (Two-hybrid), TRAPPC2L (Two-hybrid), TRAPPC2L (Two-hybrid), TRAPPC2L (Two-hybrid), REPS1 (Two-hybrid), CEP57L1 (Two-hybrid), TRAPPC2L (Affinity Capture-MS), TRAPPC2L (Affinity Capture-MS), TRAPPC2L (Affinity Capture-MS), TRAPPC2L (Two-hybrid), TRAPPC2L (Affinity Capture-MS), TRAPPC2L (Affinity Capture-MS), TRAPPC2L (Synthetic Lethality), TRAPPC2L (Affinity Capture-MS)

ESM2 similar proteins: A0JN27, A6H7F7, B2RYU6, B5FXJ6, B5FYY5, B5X7X4, B5XGE7, O43504, P55168, P61201, P61202, P61203, P79101, Q05048, Q13888, Q28F72, Q2TBL9, Q2TBV5, Q2YDH6, Q3T132, Q4KLA0, Q4R9A8, Q4VC33, Q5BJQ6, Q5F398, Q5M8X5, Q5R532, Q5R8K2, Q5R9J9, Q5RKJ1, Q63ZJ2, Q6DEG4, Q6DF40, Q6GR10, Q6IQT4, Q6IR75, Q6P1K8, Q7L5Y9, Q7SXR3, Q7ZXB7

Diamond homologs: A6H7F7, B2RYU6, B5FXJ6, B5XGE7, Q54CU7, Q5M8X5, Q5RBK9, Q9JME7, Q9UL33, Q9USZ5, O02173, A7RVK7, D3ZVF4, E2QV03, F1SRI0, P0DI81, P0DI82, P38334, Q08CN0, Q28IG8, Q3T0F2, Q54RV6, Q5RES6, Q5ZKP4, Q9CQP2, Q9VUZ1

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
TRAPPC2L	“form complex”	“TRAPP III complex, TRAPPC2 variant”	binding
TRAPPC2L	“form complex”	“TRAPP III complex, TRAPPC2B variant”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 55 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	12	40.3×	9e-15
COPII-mediated vesicle transport	7	30.9×	2e-07

GO biological processes:

GO term	Partners	Fold	FDR
obsolete vesicle tethering	10	206.5×	7e-20
COPII vesicle coat assembly	7	102.4×	2e-11
endoplasmic reticulum to Golgi vesicle-mediated transport	11	31.1×	4e-12
Golgi organization	5	13.9×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	4
Likely pathogenic	2
Uncertain significance	40
Likely benign	9
Benign	6

Top pathogenic / likely-pathogenic (6)

Variant ID	HGVS	Classification
267477	Single allele	Pathogenic
267485	Single allele	Pathogenic
619097	NM_001318525.2(TRAPPC2L):c.109G>T (p.Asp37Tyr)	Pathogenic
803287	NC_000016.10:g.89282939dup	Pathogenic
2442007	NM_001318525.2(TRAPPC2L):c.33+2T>G	Likely pathogenic
2628106	NM_001318525.2(TRAPPC2L):c.164A>T (p.Glu55Val)	Likely pathogenic

SpliceAI

1310 predictions. Top by Δscore:

Variant	Effect	Δscore
16:88856756:A:AC	donor_gain	1.0000
16:88856757:C:CC	donor_gain	1.0000
16:88856757:CGT:C	donor_gain	1.0000
16:88857181:G:GT	donor_gain	1.0000
16:88858726:G:GT	donor_gain	1.0000
16:88858747:G:GT	donor_gain	1.0000
16:88858778:G:GT	donor_gain	1.0000
16:88858781:GAC:G	donor_gain	1.0000
16:88858789:G:GT	donor_gain	1.0000
16:88859746:GCAGC:G	donor_gain	1.0000
16:88859749:GC:G	donor_gain	1.0000
16:88859751:G:GG	donor_gain	1.0000
16:88859760:G:GT	donor_gain	1.0000
16:88859889:TCAG:T	acceptor_loss	1.0000
16:88859890:CAGAT:C	acceptor_loss	1.0000
16:88859891:A:AG	acceptor_gain	1.0000
16:88859891:AGA:A	acceptor_loss	1.0000
16:88859892:G:GA	acceptor_gain	1.0000
16:88859892:GAT:G	acceptor_gain	1.0000
16:88859968:TCCAG:T	donor_loss	1.0000
16:88859969:CCAGG:C	donor_loss	1.0000
16:88859971:AGGT:A	donor_loss	1.0000
16:88859972:GG:G	donor_loss	1.0000
16:88859973:G:GA	donor_loss	1.0000
16:88859974:T:G	donor_loss	1.0000
16:88856751:CACT:C	donor_loss	0.9900
16:88856754:TCAC:T	donor_loss	0.9900
16:88856755:CACG:C	donor_loss	0.9900
16:88856756:ACG:A	donor_loss	0.9900
16:88856756:ACGT:A	donor_gain	0.9900

AlphaMissense

927 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:88858692:T:C	L36P	1.000
16:88858760:G:C	G59R	1.000
16:88858767:T:A	L61H	1.000
16:88858767:T:C	L61P	1.000
16:88859667:G:C	G71R	1.000
16:88859668:G:A	G71D	1.000
16:88859698:T:A	V81D	1.000
16:88859906:T:C	L103P	1.000
16:88857160:T:C	C4R	0.999
16:88857162:C:G	C4W	0.999
16:88857167:C:A	A6E	0.999
16:88857170:T:A	V7E	0.999
16:88858682:C:G	H33D	0.999
16:88858688:T:C	S35P	0.999
16:88858694:G:A	D37N	0.999
16:88858694:G:C	D37H	0.999
16:88858695:A:T	D37V	0.999
16:88858696:C:A	D37E	0.999
16:88858696:C:G	D37E	0.999
16:88858701:T:A	V39E	0.999
16:88858758:T:C	L58P	0.999
16:88858760:G:T	G59C	0.999
16:88858761:G:A	G59D	0.999
16:88858761:G:T	G59V	0.999
16:88859668:G:T	G71V	0.999
16:88859670:T:G	Y72D	0.999
16:88859674:T:A	V73D	0.999
16:88859677:C:T	T74I	0.999
16:88859691:A:G	K79E	0.999
16:88859693:G:C	K79N	0.999

dbSNP variants (sampled 300 via entrez): RS1000191880 (16:88860117 A>G), RS1000537276 (16:88860280 G>A,C), RS1000787347 (16:88856466 C>A,G), RS1000833242 (16:88854235 C>T), RS1000884127 (16:88854317 C>T), RS1001080162 (16:88861079 G>A,T), RS1001270148 (16:88862278 C>T), RS1001628634 (16:88860481 G>T), RS1001743452 (16:88860367 G>A), RS1002000277 (16:88855857 C>A,G,T), RS1002078643 (16:88861134 G>A,C), RS1002213070 (16:88859399 A>G), RS1002236709 (16:88854609 C>T), RS1002351272 (16:88854488 A>C,G), RS1002735179 (16:88855205 T>C)

Disease associations

OMIM: gene MIM:610970 | disease phenotypes: MIM:618331, MIM:253000

GenCC curated gene-disease

Disease	Classification	Inheritance
encephalopathy, progressive, early-onset, with episodic rhabdomyolysis	Strong	Autosomal recessive

Mondo (4): encephalopathy, progressive, early-onset, with episodic rhabdomyolysis (MONDO:0032681), mucopolysaccharidosis type 4A (MONDO:0009659), 16q24.3 microdeletion syndrome (MONDO:0016838), intellectual disability (MONDO:0001071)

Orphanet (4): Mucopolysaccharidosis type 4A (Orphanet:309297), Mucopolysaccharidosis type 4 (Orphanet:582), 16q24.3 microdeletion syndrome (Orphanet:261250), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

16 total (16 of 16 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0001250	Seizure
HP:0001344	Absent speech
HP:0002059	Cerebral atrophy
HP:0002133	Status epilepticus
HP:0002188	Delayed CNS myelination
HP:0002376	Developmental regression
HP:0002445	Tetraplegia
HP:0002540	Inability to walk
HP:0003201	Rhabdomyolysis
HP:0003236	Elevated circulating creatine kinase concentration
HP:0003593	Infantile onset
HP:0003676	Progressive
HP:0005484	Secondary microcephaly
HP:0011344	Severe global developmental delay
HP:0100704	Cerebral visual impairment

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST003479_9	Hair color	1.000000e-07
GCST009921_6	Carotid intima media thickness (mean)	4.000000e-09

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
Valproic Acid	affects cotreatment, increases expression, affects expression, increases methylation	5
aristolochic acid I	increases expression	1
bisphenol A	affects cotreatment, decreases expression	1
arsenite	affects binding, increases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
nickel sulfate	increases expression	1
epigallocatechin gallate	affects cotreatment, increases expression	1
cylindrospermopsin	increases expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	increases expression	1
Cadmium	increases expression, increases abundance	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	affects expression	1
Indomethacin	affects cotreatment, decreases expression	1
Ivermectin	decreases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Triclosan	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Cyclosporine	decreases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Lactic Acid	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3K2	Abcam HEK293T TRAPPC2L KO	Transformed cell line	Female

Clinical trials (associated diseases)

217 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
NCT01275066	PHASE3	COMPLETED	A Double-Blind Study to Evaluate the Efficacy and Safety of BMN 110 in Patients With Mucopolysaccharidosis IVA (Morquio A Syndrome)
NCT01415427	PHASE3	COMPLETED	Long-Term Efficacy and Safety Extension Study of BMN 110 in Patients With Mucopolysaccharidosis IVA (Morquio A Syndrome)
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
NCT01515956	PHASE2	COMPLETED	Study of BMN 110 in Pediatric Patients < 5 Years of Age With Mucopolysaccharidosis IVA (Morquio A Syndrome)
NCT01609062	PHASE2	TERMINATED	Safety and Exercise Study of Two Doses of BMN 110 for Morquio A Syndrome
NCT01697319	PHASE2	TERMINATED	Efficacy and Safety Study of BMN 110 for Morquio A Syndrome Patients Who Have Limited Ambulation
NCT03632213	PHASE2	UNKNOWN	Evaluation of Losartan on Cardiovascular Disease in Patients With Mucopolysaccharidoses IV A and VI
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
NCT04532047	PHASE1	RECRUITING	PEARL (PrEnAtal Enzyme Replacement Therapy for Lysosomal Storage Disorders)
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)
NCT00884949	PHASE1/PHASE2	COMPLETED	A Study to Evaluate the Safety, Tolerability and Efficacy of BMN 110 in Subjects With Mucopolysaccharidosis IVA
NCT01242111	PHASE1/PHASE2	TERMINATED	A Study to Evaluate the Long-Term Efficacy and Safety of BMN 110 in Patients With Mucopolysaccharidosis IVA (Morquio A Syndrome)
NCT05845749	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	Safety and Efficacy of Voxzogo for Growth Deficits in MPS IVA and VI
NCT00787995	Not specified	TERMINATED	A Clinical Assessment Study of Subjects With Mucopolysaccharidosis IVA (Morquio Syndrome)
NCT01457456	Not specified	WITHDRAWN	Biomarker for Morquio Disease (BioMorquio)
NCT01733615	Not specified	TERMINATED	Discovering New Biomarkers For Monitoring Disease Progression in Patients With Mucopolysaccharidosis IVA
NCT01858103	Not specified	APPROVED_FOR_MARKETING	BMN 110 US Expanded Access Program
NCT01920828	Not specified	COMPLETED	Gait Analysis in MPS IVA
NCT01961518	Not specified	COMPLETED	Screening an Orthopedic Population for Mildly-affected Individuals With Morquio Syndrome A and Maroteaux-Lamy Syndrome
NCT02153255	Not specified	WITHDRAWN	Dynamic Gait Analysis in Children With Mucopolysaccharidosis Type IVa
NCT02294877	Not specified	COMPLETED	A Multicenter, Multinational, Observational Morquio A Registry Study (MARS)
NCT05284006	Not specified	RECRUITING	Non-invasive Functional Assessment and Pathogenesis of Morquio A
NCT07361536	Not specified	RECRUITING	Cardiac Structure and Function in MPS
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