NUP54

Summary

NUP54 (nucleoporin 54, HGNC:17359) is a protein-coding gene on chromosome 4q21.1, encoding Nucleoporin p54 (Q7Z3B4). Component of the nuclear pore complex, a complex required for the trafficking across the nuclear membrane. It is a selective cancer dependency (DepMap: 79.8% of cell lines).

The nuclear envelope creates distinct nuclear and cytoplasmic compartments in eukaryotic cells. It consists of two concentric membranes perforated by nuclear pores, large protein complexes that form aqueous channels to regulate the flow of macromolecules between the nucleus and the cytoplasm. These complexes are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. This gene encodes a member of the phe-gly (FG) repeat-containing nucleoporin subset. Multiple alternatively spliced transcript variants have been found for this gene.

Source: NCBI Gene 53371 — RefSeq curated summary.

At a glance

• Gene–disease (curated): dystonia 37, early-onset, with striatal lesions (Moderate, GenCC)
• GWAS associations: 2
• Clinical variants (ClinVar): 73 total — 3 pathogenic
• Phenotypes (HPO): 48
• Cancer dependency (DepMap): dependent in 79.8% of screened cell lines
• MANE Select transcript: NM_017426

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17359
Approved symbol	NUP54
Name	nucleoporin 54
Location	4q21.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000138750
Ensembl biotype	protein_coding
OMIM	607607
Entrez	53371

Gene structure

Transcript identifiers

Ensembl transcripts: 36 — 13 protein_coding, 12 nonsense_mediated_decay, 6 protein_coding_CDS_not_defined, 5 retained_intron

ENST00000264883, ENST00000502850, ENST00000504173, ENST00000506098, ENST00000507257, ENST00000508465, ENST00000508583, ENST00000508604, ENST00000510569, ENST00000510884, ENST00000512151, ENST00000513248, ENST00000513352, ENST00000514307, ENST00000514313, ENST00000514987, ENST00000515460, ENST00000695546, ENST00000695547, ENST00000695548, ENST00000695549, ENST00000695550, ENST00000695551, ENST00000695552, ENST00000695553, ENST00000695554, ENST00000695555, ENST00000695556, ENST00000695557, ENST00000869721, ENST00000869722, ENST00000869723, ENST00000869724, ENST00000869725, ENST00000925856, ENST00000925857

RefSeq mRNA: 2 — MANE Select: NM_017426 NM_001278603, NM_017426

CCDS: CCDS3576, CCDS63998

Canonical transcript exons

ENST00000264883 — 12 exons

Exon	Start	End
ENSE00003964239	76124649	76124756
ENSE00003964240	76118075	76118194
ENSE00003964242	76130656	76130749
ENSE00003964249	76114664	76115494
ENSE00003964250	76132523	76132719
ENSE00003964251	76136186	76136412
ENSE00003964254	76144390	76144473
ENSE00003964257	76134175	76134362
ENSE00003964258	76144149	76144292
ENSE00003964260	76131230	76131284
ENSE00003964261	76148308	76148397
ENSE00003964264	76117664	76117774

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 96.89.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 36.9118 / max 377.3761, expressed in 1821 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
52641	30.2420	1817
52642	6.5227	1700
52640	0.1472	66

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	96.89	gold quality
oocyte	CL:0000023	95.92	gold quality
mucosa of paranasal sinus	UBERON:0005030	95.17	gold quality
secondary oocyte	CL:0000655	94.99	gold quality
skin of hip	UBERON:0001554	94.97	gold quality
ventricular zone	UBERON:0003053	94.81	gold quality
blood vessel layer	UBERON:0004797	94.68	gold quality
germinal epithelium of ovary	UBERON:0001304	94.52	gold quality
mucosa of sigmoid colon	UBERON:0004993	94.07	gold quality
right uterine tube	UBERON:0001302	93.97	gold quality
cerebellar hemisphere	UBERON:0002245	93.63	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.63	gold quality
cerebellar cortex	UBERON:0002129	93.58	gold quality
endometrium	UBERON:0001295	93.50	gold quality
colonic mucosa	UBERON:0000317	93.48	gold quality
cauda epididymis	UBERON:0004360	93.24	gold quality
epithelium of nasopharynx	UBERON:0001951	93.14	gold quality
oral cavity	UBERON:0000167	93.07	gold quality
cartilage tissue	UBERON:0002418	93.04	gold quality
cerebellum	UBERON:0002037	92.98	gold quality
rectum	UBERON:0001052	92.89	gold quality
embryo	UBERON:0000922	92.86	gold quality
ganglionic eminence	UBERON:0004023	92.77	gold quality
mammary duct	UBERON:0001765	92.58	gold quality
bone marrow	UBERON:0002371	92.57	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.56	gold quality
left uterine tube	UBERON:0001303	92.54	gold quality
gingival epithelium	UBERON:0001949	92.54	gold quality
right ovary	UBERON:0002118	92.54	gold quality
left ovary	UBERON:0002119	92.53	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.12
E-MTAB-7008	no	314.66

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

79 targeting NUP54, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 79.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 4)

• Mutations within the footprinted region of Nup54 polymers blocked both polymerization and binding by the PRn poly-dipeptide. 1,6-hexanediol melted FG domain polymers in vitro and reversed PRn-mediated enhancement of the nuclear pore permeability barrier, suggesting that toxicity of the PRn poly-dipeptide results in part from its ability to lock the FG repeats of nuclear pore proteins in the polymerized state. (PMID:28069952)
• Data indicate a role for nucleoporin 54 (Nup54) in the response to ionising radiation (IR) and the maintenance of homologous recombination repair mediated genome integrity. (PMID:29986057)
• Recessive NUP54 Variants Underlie Early-Onset Dystonia with Striatal Lesions. (PMID:36333996)
• CircNUP54 promotes hepatocellular carcinoma progression via facilitating HuR cytoplasmic export and stabilizing BIRC3 mRNA. (PMID:38443362)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Nup54	ENSMUSG00000034826
rattus_norvegicus	Nup54	ENSRNOG00000002247
drosophila_melanogaster	Nup54	FBGN0033737
caenorhabditis_elegans		WBGENE00003787

Protein

Protein identifiers

Nucleoporin p54 — Q7Z3B4 (reviewed: Q7Z3B4)

Alternative names: 54 kDa nucleoporin

All UniProt accessions (14): Q7Z3B4, A0A8Q3SHX2, A0A8Q3SI16, A0A8Q3WKJ4, A0A8Q3WKK2, A0A8Q3WKL3, A0A8Q3WKP8, A0A8Q3WL42, A0A8Q3WLP2, A0A8Q3WLY5, A0A8Z5F6C8, D6RB65, D6RBF7, D6RFI8

UniProt curated annotations — full annotation on UniProt →

Function. Component of the nuclear pore complex, a complex required for the trafficking across the nuclear membrane.

Subunit / interactions. Component of the p62 complex, a complex composed of NUP62, NUP54, and the isoform p58 and isoform p45 of NUP58. Interacts with NUTF2.

Subcellular location. Nucleus. Nuclear pore complex. Nucleus membrane.

Post-translational modifications. O-glycosylated.

Disease relevance. Dystonia 37, early-onset, with striatal lesions (DYT37) [MIM:620427] A form of dystonia, a disorder defined by the presence of sustained involuntary muscle contraction, often leading to abnormal postures. DYT37 is an autosomal recessive form characterized by the onset of progressive dystonia, dysphagia, and choreoathetosis in the first months or years of life. Affected individuals show delayed motor development and may have impaired intellectual development. The disease may be caused by variants affecting the gene represented in this entry.

Domain organisation. Contains FG repeats.

Similarity. Belongs to the NUP54 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q7Z3B4-1	1	yes
Q7Z3B4-2	2
Q7Z3B4-3	3

RefSeq proteins (2): NP_001265532, NP_059122* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024864	Nup54/Nup57/Nup44	Family
IPR025712	Nup54_alpha-helical_dom	Domain
IPR040985	Nup54_C	Domain

Pfam: PF13874, PF18437

UniProt features (29 total): repeat 9, sequence conflict 7, sequence variant 5, splice variant 3, helix 2, chain 1, region of interest 1, strand 1

Structure

Experimental structures (PDB)

10 structures.

PDB	Method	Resolution (Å)
7N8R	X-RAY DIFFRACTION	1.2
4JNU	X-RAY DIFFRACTION	1.45
4JO7	X-RAY DIFFRACTION	1.75
4JNV	X-RAY DIFFRACTION	1.85
4JO9	X-RAY DIFFRACTION	2.5
7R5K	ELECTRON MICROSCOPY	12
5IJN	ELECTRON MICROSCOPY	21.4
5IJO	ELECTRON MICROSCOPY	21.4
7PER	ELECTRON MICROSCOPY	35
7R5J	ELECTRON MICROSCOPY	50

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z3B4-F1	78.04	0.47

Function

Pathways and Gene Ontology

Reactome pathways

32 pathways

ID	Pathway
R-HSA-1169408	ISG15 antiviral mechanism
R-HSA-159227	Transport of the SLBP independent Mature mRNA
R-HSA-159230	Transport of the SLBP Dependant Mature mRNA
R-HSA-159231	Transport of Mature mRNA Derived from an Intronless Transcript
R-HSA-159236	Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-165054	Rev-mediated nuclear export of HIV RNA
R-HSA-168271	Transport of Ribonucleoproteins into the Host Nucleus
R-HSA-168276	NS1 Mediated Effects on Host Pathways
R-HSA-168325	Viral Messenger RNA Synthesis
R-HSA-168333	NEP/NS2 Interacts with the Cellular Export Machinery
R-HSA-170822	Regulation of Glucokinase by Glucokinase Regulatory Protein
R-HSA-180746	Nuclear import of Rev protein
R-HSA-180910	Vpr-mediated nuclear import of PICs
R-HSA-1855170	IPs transport between nucleus and cytosol
R-HSA-1855196	IP3 and IP4 transport between cytosol and nucleus
R-HSA-1855229	IP6 and IP7 transport between cytosol and nucleus
R-HSA-191859	snRNP Assembly
R-HSA-3108214	SUMOylation of DNA damage response and repair proteins
R-HSA-3232142	SUMOylation of ubiquitinylation proteins
R-HSA-3301854	Nuclear Pore Complex (NPC) Disassembly
R-HSA-3371453	Regulation of HSF1-mediated heat shock response
R-HSA-4085377	SUMOylation of SUMOylation proteins
R-HSA-4551638	SUMOylation of chromatin organization proteins
R-HSA-4570464	SUMOylation of RNA binding proteins
R-HSA-4615885	SUMOylation of DNA replication proteins
R-HSA-5619107	Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC)
R-HSA-6784531	tRNA processing in the nucleus
R-HSA-9609690	HCMV Early Events
R-HSA-9610379	HCMV Late Events
R-HSA-9615933	Postmitotic nuclear pore complex (NPC) reformation

MSigDB gene sets: 0 (showing top):

GO Biological Process (6): NLS-bearing protein import into nucleus (GO:0006607), nucleocytoplasmic transport (GO:0006913), nuclear pore organization (GO:0006999), protein localization to nuclear inner membrane (GO:0036228), mRNA transport (GO:0051028), protein transport (GO:0015031)

GO Molecular Function (2): structural constituent of nuclear pore (GO:0017056), protein binding (GO:0005515)

GO Cellular Component (6): nuclear envelope (GO:0005635), nuclear pore (GO:0005643), nuclear membrane (GO:0031965), nuclear pore central transport channel (GO:0044613), nucleus (GO:0005634), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-14 pathways:

Category	Pathways
Transport of Mature mRNAs Derived from Intronless Transcripts	3
Inositol phosphate metabolism	3
Interactions of Rev with host cellular proteins	2
Influenza Infection	2
SUMO E3 ligases SUMOylate target proteins	2
Antimicrobial mechanism of IFN-stimulated genes	1
Transport of Mature Transcript to Cytoplasm	1
Late Phase of HIV Life Cycle	1
Influenza Viral RNA Transcription and Replication	1
Export of Viral Ribonucleoproteins from Nucleus	1
Glycolysis	1
Interactions of Vpr with host cellular proteins	1
Metabolism of non-coding RNA	1
Nuclear Envelope Breakdown	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nuclear pore	2
nucleus	2
nuclear envelope	2
nuclear protein-containing complex	2
protein import into nucleus	1
nuclear transport	1
nucleus organization	1
protein-containing complex organization	1
protein localization to membrane	1
protein localization to nuclear envelope	1
RNA transport	1
transport	1
intracellular protein localization	1
establishment of protein localization	1
structural molecule activity	1
nucleocytoplasmic transport	1
binding	1
endomembrane system	1
organelle envelope	1
organelle membrane	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1986 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NUP54	NUP62	P37198	999
NUP54	NUP58	Q9BVL2	999
NUP54	NUP93	Q8N1F7	922
NUP54	NUTF2	P13662	888
NUP54	NUP35	Q8NFH5	853
NUP54	NUP214	P35658	852
NUP54	NUP98	P52948	850
NUP54	NUP88	Q99567	850
NUP54	NUP50	Q9UKX7	839
NUP54	NUP107	P57740	825
NUP54	NUP85	Q9BW27	822
NUP54	NUP43	Q8NFH3	816
NUP54	NUP205	Q92621	816
NUP54	RANBP2	P49792	797
NUP54	NUP153	P49790	791

IntAct

245 interactions, top by confidence:

A	B	Type	Score
NUP58	NUP54	psi-mi:“MI:0915”(physical association)	0.950
NUP54	NUP58	psi-mi:“MI:0915”(physical association)	0.950
NUP62	NUP54	psi-mi:“MI:0915”(physical association)	0.940
NUP54	NUP62	psi-mi:“MI:0915”(physical association)	0.940
NUP54	HGS	psi-mi:“MI:0915”(physical association)	0.780
HGS	NUP54	psi-mi:“MI:0915”(physical association)	0.780
NUP54	EXOC1	psi-mi:“MI:0915”(physical association)	0.740
rep	GTF2F2	psi-mi:“MI:0914”(association)	0.730
KRT15	NUP54	psi-mi:“MI:0915”(physical association)	0.670
NUP54	HOMER1	psi-mi:“MI:0915”(physical association)	0.670
RAN	NUP54	psi-mi:“MI:0915”(physical association)	0.670
IFT20	NUP54	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (210): NUP54 (Two-hybrid), NUP54 (Two-hybrid), NUP54 (Two-hybrid), NUP54 (Two-hybrid), IFT20 (Two-hybrid), HAUS1 (Two-hybrid), NUP54 (Affinity Capture-MS), NUP54 (Affinity Capture-Western), NUP54 (Affinity Capture-MS), NUP54 (Two-hybrid), NUP54 (Affinity Capture-MS), NUP54 (Two-hybrid), NUP54 (Two-hybrid), NUP98 (Co-fractionation), RAE1 (Co-fractionation)

ESM2 similar proteins: A1C6X5, A1CD74, A1DC51, A2R180, A4R8N4, A4RD35, A5DP36, A6R7X5, A6S9N4, A7EKZ0, B0YC95, B2AWS3, F4ID16, G0S0R2, G0S381, G0S4X2, G0SAK3, G0SBQ3, G5EEH9, O42963, P48837, P49793, P52948, P70582, Q02199, Q02629, Q02630, Q09793, Q0CPW4, Q10168, Q1DQC1, Q2H922, Q2UDY8, Q4WG58, Q55BX5, Q5B5B0, Q6C908, Q6CHN0, Q6PFD9, Q75AA0

Diamond homologs: P70582, Q7Z3B4, Q8BTS4, Q9V6B9, O42963, G0S0R2

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
NUP54	“form complex”	p62_complex	binding
NUP54	“form complex”	NPC	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 75 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
Postmitotic nuclear pore complex (NPC) reformation	6	56.9×	4e-08
NEP/NS2 Interacts with the Cellular Export Machinery	7	56.3×	5e-09
Nuclear import of Rev protein	7	54.7×	5e-09
IPs transport between nucleus and cytosol	6	53.1×	4e-08
IP3 and IP4 transport between cytosol and nucleus	6	53.1×	4e-08
IP6 and IP7 transport between cytosol and nucleus	6	53.1×	4e-08
Rev-mediated nuclear export of HIV RNA	7	51.6×	5e-09
Transport of Ribonucleoproteins into the Host Nucleus	6	49.8×	4e-08

GO biological processes:

GO term	Partners	Fold	FDR
nucleocytoplasmic transport	5	32.7×	7e-05
mRNA transport	5	21.9×	4e-04
protein import into nucleus	7	16.8×	6e-05
cell division	8	6.2×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	0
Uncertain significance	43
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
2506591	NM_017426.4(NUP54):c.1073T>G (p.Ile358Ser)	Pathogenic
2506592	NM_017426.4(NUP54):c.1126A>G (p.Lys376Glu)	Pathogenic
2506593	NM_017426.4(NUP54):c.1404ACA[2] (p.Gln471del)	Pathogenic

SpliceAI

1942 predictions. Top by Δscore:

Variant	Effect	Δscore
4:76115490:AAATG:A	acceptor_gain	1.0000
4:76115491:AATG:A	acceptor_gain	1.0000
4:76115492:ATG:A	acceptor_gain	1.0000
4:76115493:TG:T	acceptor_gain	1.0000
4:76115495:C:CC	acceptor_gain	1.0000
4:76115495:CTAGA:C	acceptor_loss	1.0000
4:76118069:GGTTA:G	donor_loss	1.0000
4:76118070:GTTAC:G	donor_loss	1.0000
4:76118071:TTA:T	donor_loss	1.0000
4:76118072:TA:T	donor_loss	1.0000
4:76118073:ACC:A	donor_loss	1.0000
4:76118074:C:A	donor_loss	1.0000
4:76130650:GCTT:G	donor_loss	1.0000
4:76130651:CTTA:C	donor_loss	1.0000
4:76130652:TTA:T	donor_loss	1.0000
4:76130653:TACAT:T	donor_loss	1.0000
4:76130654:A:AC	donor_gain	1.0000
4:76130654:ACA:A	donor_loss	1.0000
4:76130655:C:CC	donor_gain	1.0000
4:76130655:CAT:C	donor_gain	1.0000
4:76134173:A:AC	donor_gain	1.0000
4:76134174:C:CG	donor_gain	1.0000
4:76134359:CTGC:C	acceptor_gain	1.0000
4:76115489:CAAA:C	acceptor_gain	0.9900
4:76115501:CAAA:C	acceptor_gain	0.9900
4:76115502:A:T	acceptor_gain	0.9900
4:76115504:A:AC	acceptor_gain	0.9900
4:76115505:T:C	acceptor_gain	0.9900
4:76115505:T:TC	acceptor_gain	0.9900
4:76117657:CACTT:C	donor_loss	0.9900

AlphaMissense

3317 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:76131267:A:G	W309R	1.000
4:76131267:A:T	W309R	1.000
4:76136262:C:T	G149E	1.000
4:76136282:A:C	N142K	1.000
4:76136282:A:T	N142K	1.000
4:76136287:A:G	W141R	1.000
4:76136287:A:T	W141R	1.000
4:76117767:A:G	L431P	0.999
4:76117774:C:G	G429R	0.999
4:76118097:A:G	L421P	0.999
4:76118118:A:G	L414P	0.999
4:76118127:C:G	R411P	0.999
4:76118190:A:G	L390P	0.999
4:76124668:A:G	L382P	0.999
4:76124731:A:G	L361P	0.999
4:76130714:A:G	L333P	0.999
4:76131257:G:T	A312D	0.999
4:76131258:C:G	A312P	0.999
4:76131260:T:G	Q311P	0.999
4:76131265:C:A	W309C	0.999
4:76131265:C:G	W309C	0.999
4:76131266:C:G	W309S	0.999
4:76136186:C:A	K174N	0.999
4:76136186:C:G	K174N	0.999
4:76136190:A:G	F173S	0.999
4:76136204:A:C	N168K	0.999
4:76136204:A:T	N168K	0.999
4:76136217:A:G	F164S	0.999
4:76136250:C:T	G153E	0.999
4:76136251:C:A	G153W	0.999

dbSNP variants (sampled 300 via entrez): RS1000001655 (4:76130565 T>C), RS1000011117 (4:76116993 T>G), RS1000040826 (4:76143021 C>G), RS1000108170 (4:76137303 G>A), RS1000381167 (4:76125447 A>C), RS1000412211 (4:76125887 A>G), RS1000589605 (4:76141813 A>G), RS1000610517 (4:76118508 G>C), RS1000677218 (4:76119485 G>A), RS1000750156 (4:76124135 G>C,T), RS1000798649 (4:76147228 A>C), RS1001026109 (4:76137119 C>T), RS1001058499 (4:76137453 G>A,C), RS1001275114 (4:76144344 C>A,T), RS1001307486 (4:76131198 T>C)

Disease associations

OMIM: gene MIM:607607 | disease phenotypes: MIM:620427

GenCC curated gene-disease

Disease	Classification	Inheritance
dystonia 37, early-onset, with striatal lesions	Moderate	Autosomal recessive

Mondo (1): dystonia 37, early-onset, with striatal lesions (MONDO:0957385)

Orphanet (0):

HPO phenotypes

48 total (30 of 48 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000252	Microcephaly
HP:0000648	Optic atrophy
HP:0000657	Oculomotor apraxia
HP:0000750	Delayed speech and language development
HP:0001249	Intellectual disability
HP:0001251	Ataxia
HP:0001252	Hypotonia
HP:0001256	Mild intellectual disability
HP:0001257	Spasticity
HP:0001260	Dysarthria
HP:0001266	Choreoathetosis
HP:0001270	Motor delay
HP:0001276	Hypertonia
HP:0001285	Spastic tetraparesis
HP:0001288	Gait disturbance
HP:0001332	Dystonia
HP:0001336	Myoclonus
HP:0001347	Hyperreflexia
HP:0001508	Failure to thrive
HP:0002015	Dysphagia
HP:0002020	Gastroesophageal reflux
HP:0002063	Rigidity
HP:0002066	Gait ataxia
HP:0002072	Chorea
HP:0002167	Abnormal speech pattern
HP:0002273	Tetraparesis
HP:0002359	Frequent falls
HP:0002376	Developmental regression
HP:0002396	Cogwheel rigidity

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST007009_4	Hippocampal volume	3.000000e-07
GCST90000050_30	Age at first birth	6.000000e-10

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005035	hippocampal volume
EFO:0009101	age at first birth measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tretinoin	decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression	1
arsenite	affects binding, increases reaction	1
CGP 52608	affects binding, increases reaction	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Benztropine	decreases expression	1
Calcitriol	decreases expression, affects cotreatment	1
Clozapine	decreases expression	1
Cuprizone	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Haloperidol	decreases expression	1
Ivermectin	decreases expression	1
Methotrexate	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Testosterone	affects cotreatment, decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Cyclosporine	increases expression	1
Aflatoxin M1	decreases expression	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

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