NAV1

Summary

NAV1 (neuron navigator 1, HGNC:15989) is a protein-coding gene on chromosome 1q32.1, encoding Neuron navigator 1 (Q8NEY1). May be involved in neuronal migration.

This gene belongs to the neuron navigator family and is expressed predominantly in the nervous system. The encoded protein contains coiled-coil domains and a conserved AAA domain characteristic for ATPases associated with a variety of cellular activities. This gene is similar to unc-53, a Caenorhabditis elegans gene involved in axon guidance. The exact function of this gene is not known, but it is thought to play a role in in neuronal development and regeneration. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 89796 — RefSeq curated summary.

At a glance

• GWAS associations: 39
• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_001389617

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15989
Approved symbol	NAV1
Name	neuron navigator 1
Location	1q32.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314
Ensembl gene	ENSG00000134369
Ensembl biotype	protein_coding
OMIM	611628
Entrez	89796

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 9 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000367295, ENST00000367296, ENST00000367302, ENST00000430015, ENST00000438083, ENST00000469130, ENST00000477118, ENST00000490213, ENST00000491403, ENST00000685211, ENST00000850636, ENST00000855601, ENST00000935746

RefSeq mRNA: 9 — MANE Select: NM_001389617 NM_001167738, NM_001389611, NM_001389612, NM_001389613, NM_001389614, NM_001389615, NM_001389616, NM_001389617, NM_020443

CCDS: CCDS1414, CCDS53456, CCDS91142

Canonical transcript exons

ENST00000685211 — 34 exons

Exon	Start	End
ENSE00001444139	201648634	201649425
ENSE00002286719	201819837	201826969
ENSE00002332765	201812465	201812661
ENSE00002335957	201808418	201808610
ENSE00002347173	201809164	201809261
ENSE00002351889	201712817	201712919
ENSE00002358078	201811903	201811974
ENSE00002371738	201809442	201809537
ENSE00002375869	201718390	201718755
ENSE00002381167	201808703	201808871
ENSE00002388282	201803593	201803714
ENSE00002390902	201809946	201810105
ENSE00002399112	201790554	201790577
ENSE00002401323	201810523	201810758
ENSE00002401668	201804489	201804497
ENSE00002406981	201817088	201817285
ENSE00002416205	201811603	201811757
ENSE00002419782	201807953	201808149
ENSE00002428325	201813140	201813258
ENSE00003037462	201622853	201623606
ENSE00003458302	201789740	201789792
ENSE00003463171	201785310	201785351
ENSE00003494767	201780421	201780559
ENSE00003505080	201790689	201790766
ENSE00003516675	201788468	201788638
ENSE00003531715	201781012	201781309
ENSE00003571117	201786429	201786577
ENSE00003578272	201782176	201782869
ENSE00003588273	201794466	201794577
ENSE00003624602	201793792	201793875
ENSE00003651977	201783406	201783852
ENSE00003922520	201588539	201588649
ENSE00003925175	201539127	201539342
ENSE00003925478	201629404	201629507

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 96.95.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.4830 / max 1086.5830, expressed in 1574 samples.

FANTOM5 promoters (33 alternative TSS)

Promoter ID	TPM avg	Samples expressed
7745	6.3689	1056
7723	5.5407	926
7718	5.0663	985
7720	3.0951	987
7735	3.0140	417
7746	1.7942	715
7743	1.3894	726
7740	1.1214	382
7750	0.8989	456
7736	0.5146	165

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	96.95	gold quality
lateral globus pallidus	UBERON:0002476	96.92	gold quality
left ventricle myocardium	UBERON:0006566	96.68	gold quality
lateral nuclear group of thalamus	UBERON:0002736	96.46	gold quality
saphenous vein	UBERON:0007318	96.43	gold quality
substantia nigra pars reticulata	UBERON:0001966	96.38	gold quality
Brodmann (1909) area 23	UBERON:0013554	96.35	gold quality
dorsal plus ventral thalamus	UBERON:0001897	96.02	gold quality
middle temporal gyrus	UBERON:0002771	96.01	gold quality
inferior vagus X ganglion	UBERON:0005363	95.99	gold quality
pericardium	UBERON:0002407	95.87	gold quality
synovial joint	UBERON:0002217	95.70	gold quality
medulla oblongata	UBERON:0001896	95.56	gold quality
ventral tegmental area	UBERON:0002691	95.47	gold quality
subthalamic nucleus	UBERON:0001906	95.43	gold quality
substantia nigra pars compacta	UBERON:0001965	95.23	gold quality
epithelial cell of pancreas	CL:0000083	94.80	silver quality
superior vestibular nucleus	UBERON:0007227	94.74	gold quality
tendon of biceps brachii	UBERON:0008188	94.58	gold quality
globus pallidus	UBERON:0001875	94.25	gold quality
entorhinal cortex	UBERON:0002728	94.25	gold quality
sural nerve	UBERON:0015488	94.23	gold quality
cortical plate	UBERON:0005343	94.18	gold quality
layer of synovial tissue	UBERON:0007616	93.99	gold quality
medial globus pallidus	UBERON:0002477	93.55	gold quality
descending thoracic aorta	UBERON:0002345	93.52	gold quality
cauda epididymis	UBERON:0004360	93.42	gold quality
trigeminal ganglion	UBERON:0001675	93.17	gold quality
corpus callosum	UBERON:0002336	93.07	gold quality
vena cava	UBERON:0004087	92.97	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	57.23
E-GEOD-84465	yes	27.13
E-CURD-119	yes	23.66
E-HCAD-25	yes	16.68
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PAX6

miRNA regulators (miRDB)

381 targeting NAV1, 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-6867-5P	100.00	82.21	3464
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-371B-5P	99.99	75.34	4759

Literature-anchored findings (GeneRIF, showing 6)

• cloning of the gene neuron navigator-1 (NAV1), a human homolog of unc-53, a gene involved in axon guidance in Caenorhabditis elegans (PMID:12079279)
• NAV1 forms a complex with the RhoGEF TRIO and the +TIP EB1 on the plus ends of growing microtubules, and regulates TRIO-mediated Rac1 activation and neurite outgrowth. (PMID:25065758)
• The +TIP Navigator 1 (NAV1) is important for neurite outgrowth and interacts and colocalizes with TRIO, a Rho guanine nucleotide exchange factor that enables neurite outgrowth by activating the Rho GTPases Rac1 and RhoG. (PMID:25065758)
• Genetic Association Analyses Highlight IL6, ALPL, and NAV1 As 3 New Susceptibility Genes Underlying Calcific Aortic Valve Stenosis. (PMID:32141789)
• Nav1.7 as a chondrocyte regulator and therapeutic target for osteoarthritis. (PMID:38172636)
• Functional Characteristics of the Nav1.1 p.Arg1596Cys Mutation Associated with Varying Severity of Epilepsy Phenotypes. (PMID:38339022)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	nav1b	ENSDARG00000058771
danio_rerio	NAV1	ENSDARG00000078011
mus_musculus	Nav1	ENSMUSG00000009418
rattus_norvegicus	Nav1	ENSRNOG00000008425
caenorhabditis_elegans		WBGENE00006788

Paralogs (2): NAV3 (ENSG00000067798), NAV2 (ENSG00000166833)

Protein

Protein identifiers

Neuron navigator 1 — Q8NEY1 (reviewed: Q8NEY1)

Alternative names: Pore membrane and/or filament-interacting-like protein 3, Steerin-1, Unc-53 homolog 1

All UniProt accessions (6): A0A0A0MRJ3, A0A8I5KSE4, Q8NEY1, H0Y6F6, H0YA94, H7BZD9

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in neuronal migration.

Subunit / interactions. Interacts with tubulin.

Subcellular location. Cytoplasm. Cytoskeleton.

Tissue specificity. Broadly expressed at low levels. Expressed at high levels in heart, skeletal muscle, placenta and possibly in pancreas and liver.

Similarity. Belongs to the Nav/unc-53 family.

Isoforms (7)

UniProt ID	Names	Canonical?
Q8NEY1-1	1	yes
Q8NEY1-2	2
Q8NEY1-3	3
Q8NEY1-4	4
Q8NEY1-5	5
Q8NEY1-6	6
Q8NEY1-7	7

RefSeq proteins (9): NP_001161210, NP_001376540, NP_001376541, NP_001376542, NP_001376543, NP_001376544, NP_001376545, NP_001376546, NP_065176 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003593	AAA+_ATPase	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR039041	Nav/unc-53	Family
IPR057126	NAV1-like_ubiquitin-like	Domain
IPR057568	CortBP2_NAV1-like_AAA_lid	Domain

Pfam: PF23092, PF25408

UniProt features (86 total): modified residue 34, compositionally biased region 20, region of interest 9, splice variant 7, sequence conflict 7, coiled-coil region 4, sequence variant 4, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NEY1-F1	50.18	0.08

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 (34): 1, 90, 142, 152, 159, 194, 199, 296, 308, 312, 362, 391, 452, 474, 476, 490, 528, 534, 541, 544 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 276 (showing top): GCACCTT_MIR18A_MIR18B, TGGTGCT_MIR29A_MIR29B_MIR29C, GAANYNYGACNY_UNKNOWN, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, RORA1_01, GOBP_NEUROGENESIS, CAGCTG_AP4_Q5, GTGCCTT_MIR506, RICKMAN_METASTASIS_DN, SOX9_B1, GROSS_HYPOXIA_VIA_ELK3_ONLY_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX4_UP, SCHAEFFER_SOX9_TARGETS_IN_PROSTATE_DEVELOPMENT_DN, GOBP_NEURON_MIGRATION

GO Biological Process (5): microtubule bundle formation (GO:0001578), neuron migration (GO:0001764), nervous system development (GO:0007399), neurogenesis (GO:0022008), cell differentiation (GO:0030154)

GO Molecular Function (2): protein binding (GO:0005515), ATP hydrolysis activity (GO:0016887)

GO Cellular Component (5): microtubule (GO:0005874), microtubule cytoskeleton (GO:0015630), axon initial segment (GO:0043194), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
microtubule cytoskeleton organization	1
cell migration	1
generation of neurons	1
system development	1
nervous system development	1
cell differentiation	1
cellular developmental process	1
binding	1
ribonucleoside triphosphate phosphatase activity	1
ATP-dependent activity	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1
cytoskeleton	1
main axon	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1120 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NAV1	SCN1A	P35498	960
NAV1	SCN8A	Q9UQD0	936
NAV1	SCN4A	P35499	899
NAV1	SCN2A	Q99250	871
NAV1	SCN9A	Q15858	816
NAV1	SCN3A	Q9NY46	814
NAV1	SCN5A	Q14524	812
NAV1	SCN2B	O60939	769
NAV1	ANK3	Q12955	730
NAV1	SCN10A	Q9Y5Y9	726
NAV1	SCN11A	Q9UI33	722
NAV1	KCNH2	Q12809	655
NAV1	BACE1	P56817	646
NAV1	SCN4B	Q8IWT1	643
NAV1	KCNMB1	P78475	593

IntAct

144 interactions, top by confidence:

A	B	Type	Score
MED4	MED19	psi-mi:“MI:2364”(proximity)	0.900
MAP3K14	IKBKB	psi-mi:“MI:0914”(association)	0.900
VAPB	FAM83G	psi-mi:“MI:0914”(association)	0.730
YWHAG	BLTP3B	psi-mi:“MI:0914”(association)	0.640
YWHAG	BLTP3B	psi-mi:“MI:2364”(proximity)	0.640
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
YWHAB	BLTP3B	psi-mi:“MI:2364”(proximity)	0.610
YWHAB	BLTP3B	psi-mi:“MI:0914”(association)	0.610
SLC16A3	CASK	psi-mi:“MI:0914”(association)	0.590
YWHAH	BLTP3B	psi-mi:“MI:0914”(association)	0.570
YWHAH	BLTP3B	psi-mi:“MI:2364”(proximity)	0.570
WASHC3	WASH3P	psi-mi:“MI:0914”(association)	0.530
DISC1	AP4M1	psi-mi:“MI:0914”(association)	0.530
COG6	EXOC5	psi-mi:“MI:0914”(association)	0.530
APLNR	SLC33A1	psi-mi:“MI:0914”(association)	0.530
NAV1	YWHAE	psi-mi:“MI:0915”(physical association)	0.470
SFN	NAV1	psi-mi:“MI:0915”(physical association)	0.470
NAV1	ERP29	psi-mi:“MI:0915”(physical association)	0.400
TBC1D4	NAV1	psi-mi:“MI:0915”(physical association)	0.370
ECE1	NAV1	psi-mi:“MI:0915”(physical association)	0.370
	PGRMC1	psi-mi:“MI:0914”(association)	0.350
PB2	ESYT2	psi-mi:“MI:0914”(association)	0.350
YWHAB	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
YWHAG	C1orf226	psi-mi:“MI:0914”(association)	0.350
YWHAQ	SHTN1	psi-mi:“MI:0914”(association)	0.350
CEP192	WASL	psi-mi:“MI:0914”(association)	0.350

BioGRID (201): NAV1 (Two-hybrid), NAV1 (Two-hybrid), NAV1 (Affinity Capture-MS), NAV1 (Affinity Capture-MS), NAV1 (Affinity Capture-MS), PPA1 (Co-fractionation), PPA2 (Co-fractionation), NAV1 (Proximity Label-MS), NAV1 (Proximity Label-MS), NAV1 (Proximity Label-MS), NAV1 (Proximity Label-MS), NAV1 (Proximity Label-MS), NAV1 (Proximity Label-MS), NAV1 (Affinity Capture-MS), NAV1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8H8C0, A0A1L8HFX9, A0A2K1J5A5, A0A2R6X6S3, A0JM08, A2RUV4, B1AZP2, F1QIC4, O14490, O61366, P46012, P46582, P70047, P83510, P97836, P97839, Q01538, Q08D57, Q09314, Q09599, Q0KIC3, Q18221, Q1LY77, Q498L0, Q501J7, Q52KW0, Q5F3P8, Q5RAU1, Q5SW79, Q5TZ18, Q5XHF3, Q66J90, Q69Z38, Q6A065, Q6DFG0, Q6PEI3, Q71M21, Q80TN7, Q86TC9, Q8CFC2

Diamond homologs: A5D7D1, L7UZ85, O13728, O43707, O76329, O88990, P05094, P05095, P12814, P13466, P18091, P57780, Q08043, Q0III9, Q155Q3, Q1ZXH8, Q2PFV7, Q2VUH7, Q3B7N2, Q550R2, Q5RCS6, Q5TZ18, Q7PKQ5, Q7TPR4, Q80TN7, Q8CH77, Q8IVL0, Q8IVL1, Q8NEY1, Q90734, Q9QXQ0, Q9VIQ9, Q9Y0T3, Q9Z1P2, D3ZHA0, D3ZHV2, O75369, P21333, Q07DZ5, Q14315

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 163 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	8	49.3×	7e-10
Activation of BAD and translocation to mitochondria	7	48.9×	7e-09
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	43.1×	2e-08
Activation of BH3-only proteins	7	31.9×	1e-07
RHO GTPases activate PKNs	8	23.3×	1e-07
Intrinsic Pathway for Apoptosis	8	21.5×	1e-07
Oncogenic MAPK signaling	7	15.9×	8e-06
FOXO-mediated transcription	5	15.4×	3e-04

GO biological processes:

GO term	Partners	Fold	FDR
protein targeting	8	20.1×	3e-06
intracellular protein localization	13	9.3×	2e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	27
Likely benign	3
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

4772 predictions. Top by Δscore:

Variant	Effect	Δscore
1:201712812:A:AG	acceptor_gain	1.0000
1:201712813:C:G	acceptor_gain	1.0000
1:201712815:A:AG	acceptor_gain	1.0000
1:201712815:A:T	acceptor_loss	1.0000
1:201712816:G:GA	acceptor_gain	1.0000
1:201712816:GA:G	acceptor_gain	1.0000
1:201712816:GAC:G	acceptor_gain	1.0000
1:201712816:GACCC:G	acceptor_gain	1.0000
1:201712917:CAGGT:C	donor_loss	1.0000
1:201712918:AGGTA:A	donor_loss	1.0000
1:201712919:GGT:G	donor_loss	1.0000
1:201712920:GTAAG:G	donor_loss	1.0000
1:201712921:T:G	donor_loss	1.0000
1:201718384:A:AG	acceptor_gain	1.0000
1:201718385:C:G	acceptor_gain	1.0000
1:201718385:CCCA:C	acceptor_loss	1.0000
1:201718386:CCAGC:C	acceptor_loss	1.0000
1:201718387:CA:C	acceptor_loss	1.0000
1:201718388:A:AC	acceptor_loss	1.0000
1:201718388:A:AG	acceptor_gain	1.0000
1:201718389:G:GT	acceptor_gain	1.0000
1:201718389:GC:G	acceptor_gain	1.0000
1:201718389:GCT:G	acceptor_gain	1.0000
1:201718389:GCTC:G	acceptor_gain	1.0000
1:201718389:GCTCC:G	acceptor_gain	1.0000
1:201718753:CGGG:C	donor_loss	1.0000
1:201718754:GG:G	donor_gain	1.0000
1:201718755:GG:G	donor_gain	1.0000
1:201718755:GGT:G	donor_loss	1.0000
1:201718756:G:C	donor_loss	1.0000

AlphaMissense

14069 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:201649372:T:C	L235P	1.000
1:201649387:T:C	L240P	1.000
1:201649389:G:A	G241R	1.000
1:201649389:G:C	G241R	1.000
1:201649390:G:T	G241V	1.000
1:201649393:A:C	D242A	1.000
1:201649393:A:G	D242G	1.000
1:201649393:A:T	D242V	1.000
1:201649396:T:C	L243P	1.000
1:201649399:A:T	E244V	1.000
1:201649405:T:C	L246P	1.000
1:201712853:T:A	V265D	1.000
1:201712862:T:A	L268H	1.000
1:201712862:T:C	L268P	1.000
1:201712865:G:C	R269P	1.000
1:201712874:T:C	L272P	1.000
1:201780443:A:C	S417R	1.000
1:201780445:T:A	S417R	1.000
1:201780445:T:G	S417R	1.000
1:201790702:T:C	L1086P	1.000
1:201790714:T:C	L1090P	1.000
1:201790756:T:C	L1104P	1.000
1:201793799:T:C	L1110P	1.000
1:201793810:T:C	F1114L	1.000
1:201793811:T:C	F1114S	1.000
1:201793812:T:A	F1114L	1.000
1:201793812:T:G	F1114L	1.000
1:201793823:T:C	L1118P	1.000
1:201793844:T:C	L1125P	1.000
1:201794476:T:C	L1139P	1.000

dbSNP variants (sampled 300 via entrez): RS1000005685 (1:201810932 C>T), RS1000034943 (1:201719525 A>C), RS1000056753 (1:201589637 G>A), RS1000068612 (1:201631301 G>A), RS1000090970 (1:201675956 C>T), RS1000102503 (1:201609657 T>C), RS1000105439 (1:201569779 A>G), RS1000110306 (1:201735532 A>C), RS1000135602 (1:201713792 G>A), RS1000136324 (1:201635054 T>G), RS1000148431 (1:201584774 C>T), RS1000165881 (1:201564678 C>T), RS1000171381 (1:201688236 G>A), RS1000209958 (1:201744152 G>A), RS1000235072 (1:201737677 C>T)

Disease associations

OMIM: gene MIM:611628 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): autism spectrum disorder (MONDO:0005258)

Orphanet (1): NON RARE IN EUROPE: Autism (Orphanet:106)

HPO phenotypes

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

GWAS associations

39 associations (top):

Study	Trait	p-value
GCST001762_585	Obesity-related traits	8.000000e-06
GCST002112_15	Celiac disease	6.000000e-06
GCST002783_103	Body mass index	5.000000e-06
GCST002783_185	Body mass index	2.000000e-10
GCST002783_338	Body mass index	5.000000e-10
GCST002783_587	Body mass index	2.000000e-08
GCST004065_23	Waist circumference	2.000000e-08
GCST004065_6	Waist circumference	7.000000e-07
GCST004495_57	BMI (adjusted for smoking behaviour)	1.000000e-07
GCST004495_58	BMI (adjusted for smoking behaviour)	5.000000e-11
GCST004495_59	BMI (adjusted for smoking behaviour)	6.000000e-06
GCST004497_14	Body mass index (joint analysis main effects and smoking interaction)	2.000000e-10
GCST004497_15	Body mass index (joint analysis main effects and smoking interaction)	4.000000e-07
GCST004499_84	BMI in non-smokers	8.000000e-07
GCST004499_85	BMI in non-smokers	1.000000e-09
GCST004557_153	Body mass index	5.000000e-09
GCST004557_258	Body mass index	1.000000e-06
GCST004557_36	Body mass index	1.000000e-08
GCST004557_80	Body mass index	5.000000e-06
GCST004558_220	Body mass index (joint analysis main effects and physical activity interaction)	1.000000e-08
GCST004558_53	Body mass index (joint analysis main effects and physical activity interaction)	6.000000e-06
GCST004558_72	Body mass index (joint analysis main effects and physical activity interaction)	4.000000e-09
GCST004559_150	Body mass index in physically active individuals	4.000000e-08
GCST004559_69	Body mass index in physically active individuals	7.000000e-09
GCST006802_5	Body mass index	4.000000e-06
GCST006940_101	Neurociticism	3.000000e-08
GCST006979_967	Heel bone mineral density	6.000000e-12
GCST007096_167	Pulse pressure	1.000000e-10
GCST007268_78	Diastolic blood pressure	5.000000e-10
GCST007269_60	Pulse pressure	3.000000e-14

EFO canonical traits (12, from GWAS)

EFO ID	Trait name
EFO:0004697	estradiol measurement
EFO:0004340	body mass index
EFO:0004318	smoking behavior
EFO:0008002	physical activity measurement
EFO:0007660	neuroticism measurement
EFO:0009270	heel bone mineral density
EFO:0005763	pulse pressure measurement
EFO:0006336	diastolic blood pressure
EFO:0007876	insomnia measurement
EFO:0000266	aortic stenosis
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004531	urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases expression	7
methylmercuric chloride	decreases expression, increases expression, affects cotreatment	4
trichostatin A	affects cotreatment, decreases expression, increases expression	3
sodium arsenite	increases abundance, increases stability, decreases expression, affects cotreatment	3
Benzo(a)pyrene	affects methylation, decreases expression, affects cotreatment	3
Aflatoxin B1	decreases expression, decreases methylation, increases methylation, decreases reaction	3
bisphenol A	decreases methylation, increases expression	2
mercuric bromide	decreases expression, affects cotreatment	2
entinostat	affects cotreatment, decreases expression, increases expression	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	2
bisphenol S	increases expression, affects cotreatment, decreases expression	2
Vorinostat	decreases expression, affects cotreatment	2
Panobinostat	affects cotreatment, decreases expression	2
Cisplatin	decreases expression, affects cotreatment	2
Dexamethasone	decreases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	affects expression, increases methylation	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression	1
arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	decreases expression	1
manganese chloride	decreases expression, increases abundance, affects cotreatment	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
CGP 52608	affects binding, increases reaction	1
deguelin	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00391261	PHASE4	COMPLETED	An Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT01028820	PHASE4	COMPLETED	FMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01333865	PHASE4	COMPLETED	A Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700	PHASE4	COMPLETED	Milnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200	PHASE4	COMPLETED	Omega-3 Fatty Acids in Autism Spectrum Disorders
NCT02096952	PHASE4	COMPLETED	Methylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02235467	PHASE4	COMPLETED	Multisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02940574	PHASE4	COMPLETED	Neural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629	PHASE4	COMPLETED	Promoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646	PHASE4	COMPLETED	Evaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431	PHASE4	COMPLETED	Improving Driving in Young People With Autism Spectrum Disorders
NCT03757585	PHASE4	COMPLETED	Natural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353	PHASE4	COMPLETED	Pragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656	PHASE4	COMPLETED	Biomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245	PHASE4	UNKNOWN	Safety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339	PHASE4	RECRUITING	AWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052	PHASE4	TERMINATED	A Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665	PHASE4	RECRUITING	The TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697	PHASE4	COMPLETED	Pilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804	PHASE4	COMPLETED	Pilot RCT Using Homeopathic Medicines in ASD
NCT07439042	PHASE4	NOT_YET_RECRUITING	Buspirone for Anxiety in Autistic Youth
NCT01302964	PHASE3	COMPLETED	Mirtazapine Treatment of Anxiety in Children and Adolescents With Pervasive Developmental Disorders
NCT01706523	PHASE3	TERMINATED	Open Label Extension Study of STX209 (Arbaclofen) in Autism Spectrum Disorders
NCT01825798	PHASE3	COMPLETED	Treatment of Overweight Induced by Antipsychotic Medication in Young People With Autism Spectrum Disorders (ASD)
NCT01972074	PHASE3	COMPLETED	Behavioral and Neural Response to Memantine in Adolescents With Autism Spectrum Disorder
NCT02985749	PHASE3	COMPLETED	A Study of Oxytocin for the Treatment of Social Impairment in Individuals With High Functioning Autism Spectrum Disorder
NCT03197922	PHASE3	COMPLETED	Treatment of Encopresis in Children With Autism Spectrum Disorders
NCT03504917	PHASE3	TERMINATED	A Study of Balovaptan in Adults With Autism Spectrum Disorder With a 2-Year Open-Label Extension
NCT03553875	PHASE3	TERMINATED	Memantine for the Treatment of Social Deficits in Youth With Disorders of Impaired Social Interactions
NCT03640156	PHASE3	COMPLETED	Modulating Socially Adaptive Mirror System Functioning in Autism by Oxytocin
NCT03715153	PHASE3	TERMINATED	Efficacy and Safety of Bumetanide Oral Liquid Formulation in Children Aged From 2 to Less Than 7 Years Old With Autism Spectrum Disorder.
NCT03715166	PHASE3	TERMINATED	Efficacy and Safety of Bumetanide Oral Liquid Formulation in Children and Adolescents Aged From 7 to Less Than 18 Years Old With Autism Spectrum Disorder
NCT04233502	PHASE3	WITHDRAWN	Efficacy and Safety of Slenyto for Insomnia in Children With ASD
NCT04578756	PHASE3	COMPLETED	Open-Label, Flexible-dose Study to Evaluate the Long-Term Safety and Tolerability of Cariprazine in the Treatment of Pediatric Participants With Schizophrenia, Bipolar I Disorder, or Autism Spectrum Disorder
NCT04623398	PHASE3	COMPLETED	Effect of Lithium in Patients With Autism Spectrum Disorder and Phelan-McDermid Syndrome (SHANK3 Haploinsufficiency)
NCT04725383	PHASE3	TERMINATED	Amitriptyline for Repetitive Behaviors in Autism Spectrum Disorders
NCT05212493	PHASE3	COMPLETED	The Effects of Medical Cannabis in Children With Autistic Spectrum Disorder
NCT05361707	PHASE3	UNKNOWN	Evaluating the Effects of Tasimelteon in Individuals With Autism Spectrum Disorder (ASD) and Sleep Disturbances
NCT05439616	PHASE3	COMPLETED	Study of Cariprazine Oral Capsules or Solution to Assess Adverse Events and Change in Irritability Due to Autism Spectrum Disorder (ASD) in Participants Aged 5-17 Years With ASD
NCT06229210	PHASE3	RECRUITING	Safety and Tolerability Trial of Lumateperone in Pediatric Patients With Schizophrenia, Bipolar Disorder or Autism Spectrum Disorder