NINL

Summary

NINL (ninein like, HGNC:29163) is a protein-coding gene on chromosome 20p11.21, encoding Ninein-like protein (Q9Y2I6). Involved in the microtubule organization in interphase cells.

Predicted to enable calcium ion binding activity. Predicted to be involved in microtubule anchoring at centrosome. Located in centrosome.

Source: NCBI Gene 22981 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 284 total
• MANE Select transcript: NM_025176

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29163
Approved symbol	NINL
Name	ninein like
Location	20p11.21
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0980, NLP
Ensembl gene	ENSG00000101004
Ensembl biotype	protein_coding
OMIM	609580
Entrez	22981

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 16 protein_coding, 6 protein_coding_CDS_not_defined, 5 retained_intron, 2 nonsense_mediated_decay

ENST00000278886, ENST00000336104, ENST00000461642, ENST00000464285, ENST00000489780, ENST00000496509, ENST00000706718, ENST00000706719, ENST00000706720, ENST00000706721, ENST00000706722, ENST00000706723, ENST00000706724, ENST00000706725, ENST00000706726, ENST00000889359, ENST00000889360, ENST00000889361, ENST00000889362, ENST00000889363, ENST00000889364, ENST00000889365, ENST00000924903, ENST00000924904, ENST00000924905, ENST00000960977, ENST00000960978, ENST00000960979, ENST00000960980

RefSeq mRNA: 2 — MANE Select: NM_025176 NM_001318226, NM_025176

CCDS: CCDS33452, CCDS82605

Canonical transcript exons

ENST00000278886 — 24 exons

Exon	Start	End
ENSE00000897176	25467389	25467458
ENSE00000897181	25469991	25470095
ENSE00000897185	25476043	25477089
ENSE00000897252	25503952	25504104
ENSE00000897275	25517753	25517849
ENSE00001140027	25480161	25480267
ENSE00001140053	25512834	25513006
ENSE00001160109	25452697	25453642
ENSE00001285305	25481968	25482100
ENSE00001285336	25498210	25498346
ENSE00001285343	25500840	25501010
ENSE00001285368	25504888	25505078
ENSE00001285376	25510674	25510740
ENSE00001358765	25478923	25479206
ENSE00001358809	25526408	25526598
ENSE00003502001	25461522	25461635
ENSE00003529051	25458383	25458529
ENSE00003539090	25496663	25496803
ENSE00003551023	25491351	25491525
ENSE00003600083	25455673	25455786
ENSE00003601946	25489875	25489985
ENSE00003615795	25489244	25489324
ENSE00003786747	25462383	25462541
ENSE00003850513	25585455	25585531

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 94.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.2253 / max 65.0649, expressed in 1347 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
186807	4.9153	1324
186803	0.2054	85
186804	0.0708	42
186802	0.0266	14
186805	0.0072	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
renal medulla	UBERON:0000362	94.29	gold quality
ventricular zone	UBERON:0003053	93.24	gold quality
cerebellar hemisphere	UBERON:0002245	91.75	gold quality
cerebellar cortex	UBERON:0002129	91.69	gold quality
right hemisphere of cerebellum	UBERON:0014890	91.62	gold quality
left ovary	UBERON:0002119	91.15	gold quality
cerebellum	UBERON:0002037	90.52	gold quality
ganglionic eminence	UBERON:0004023	89.88	gold quality
metanephros cortex	UBERON:0010533	89.85	gold quality
right ovary	UBERON:0002118	89.22	gold quality
ovary	UBERON:0000992	88.27	gold quality
cortical plate	UBERON:0005343	87.54	gold quality
cervix squamous epithelium	UBERON:0006922	87.29	silver quality
adult mammalian kidney	UBERON:0000082	87.27	gold quality
right adrenal gland cortex	UBERON:0035827	87.02	gold quality
right lobe of thyroid gland	UBERON:0001119	86.86	gold quality
pituitary gland	UBERON:0000007	86.85	gold quality
lower esophagus mucosa	UBERON:0035834	86.85	gold quality
left lobe of thyroid gland	UBERON:0001120	86.81	gold quality
right adrenal gland	UBERON:0001233	86.73	gold quality
thyroid gland	UBERON:0002046	86.45	gold quality
tibia	UBERON:0000979	86.40	gold quality
right lobe of liver	UBERON:0001114	85.97	gold quality
adenohypophysis	UBERON:0002196	85.90	gold quality
muscle layer of sigmoid colon	UBERON:0035805	85.85	gold quality
adrenal cortex	UBERON:0001235	85.84	gold quality
descending thoracic aorta	UBERON:0002345	85.65	gold quality
ascending aorta	UBERON:0001496	85.61	gold quality
kidney	UBERON:0002113	85.61	gold quality
caput epididymis	UBERON:0004358	85.57	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting NINL, 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-186-5P	99.99	70.83	3707
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-1825	99.72	68.11	1089
HSA-MIR-3660	99.68	67.33	1149
HSA-MIR-4526	99.68	67.07	1136
HSA-MIR-5197-5P	99.64	69.08	1494
HSA-MIR-199A-5P	99.51	69.71	1107
HSA-MIR-199B-5P	99.51	69.74	1098
HSA-MIR-5689	99.50	71.26	1154
HSA-MIR-6128	99.33	67.83	1581
HSA-MIR-5693	99.24	66.67	1106
HSA-MIR-10399-5P	99.17	69.87	2610
HSA-MIR-6504-3P	99.17	69.31	2891

Literature-anchored findings (GeneRIF, showing 13)

• Overexpression of ninein and the ninein-like protein NIP induces fragmentation of the Golgi and causes lysosomes to disperse toward the cell periphery. (PMID:16254247)
• results indicate that ninein-like protein expression is cell cycle-dependent and regulated by anaphase-promoting cyclosome complex-mediated protein degradation (PMID:17403670)
• Overexpression of Nlp in ovarian tumors raises the possibility that Nlp may play a role in ovarian carcinogenesis. (PMID:18538832)
• Nlp(isoB)interacts with USH2A and lebercilin. (PMID:18826961)
• BRCA1 interaction of Nlp might be required for the successful mitotic progression, and abnormalities of Nlp lead to genomic instability. (PMID:19509300)
• Nlp overexpression might contribute to the development of head and neck squamous cell carcinoma (PMID:19724857)
• Nlp abnormalities may contribute to genomic instability and tumorigenesis and might serve as a potential biomarker for clinical diagnosis and as a therapeutic target. (PMID:20093778)
• regulation of Nlp by Aurora B is critical for the completion of cytokinesis, providing novel insights into understanding the machinery of cell cycle progression. (PMID:20864540)
• findings demonstrate that Cdc2/cyclin B1 is a key regulator in maintaining appropriate degradation and subcellular localization of Nlp, providing novel insights into understanding on the role of Cdc2/cyclin B1 in mitotic progression (PMID:20890132)
• This review summarises our current knowledge of physiological roles of Nlp, with an emphasis on its potentials in tumourigenesis. (PMID:21505454)
• Breast cancer patients with high expression of Nlp were likely resistant to the treatment of paclitaxel. (PMID:22353935)
• these data support a model where CC2D2A associates with NINL to provide a docking point for cilia-directed cargo vesicles, suggesting a mechanism by which transition zone proteins can control the protein content of the ciliary compartment. (PMID:26485645)
• Upon UVC radiation, Nlp interacts with XPA and ERCC1, and enhances their association (PMID:26805762)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ninl	ENSDARG00000098414
mus_musculus	Ninl	ENSMUSG00000068115
rattus_norvegicus	Ninl	ENSRNOG00000027747
drosophila_melanogaster	Nin	FBGN0000228
caenorhabditis_elegans		WBGENE00011444

Paralogs (1): NIN (ENSG00000100503)

Protein

Protein identifiers

Ninein-like protein — Q9Y2I6 (reviewed: Q9Y2I6)

All UniProt accessions (4): Q9Y2I6, A0A9L9PXF7, A0A9L9PYA0, H0Y2V7

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the microtubule organization in interphase cells. Overexpression induces the fragmentation of the Golgi, and causes lysosomes to disperse toward the cell periphery; it also interferes with mitotic spindle assembly. Involved in vesicle transport in photoreceptor cells. May play a role in ovarian carcinogenesis.

Subunit / interactions. Interacts with gamma-tubulin and TUBGCP4. Interacts with anaphase promoting complex/cyclosome (APC/C). Interacts with CDC20 and FZR1. Isoform 2 interacts with LCA5 and USH2A. Isoform 2 interacts with DZANK1.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome.

Tissue specificity. Expressed in KYSE-150 esophageal carcinoma, HeLa cervical carcinoma and U2OS osteosarcoma cells. Expression is regulated in a cell cycle-dependent manner and peaks during G2/M phase (at protein level). Expressed in fetal heart, skeletal muscle, liver, lung and cochlea, and in adult brain, testis, kidney and retina.

Post-translational modifications. Phosphorylated by PLK1 which disrupts its centrosome association and interaction with gamma-tubulin. Ubiquitinated by the APC/C complex leading to its degradation.

Domain organisation. The KEN and D (destructive) boxes are required for the cell cycle-controlled NINL degradation by the APC/C pathway.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y2I6-1	1, NLP(isoA)	yes
Q9Y2I6-2	2, NLP(isoB)

RefSeq proteins (2): NP_001305155, NP_079452* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002048	EF_hand_dom	Domain
IPR011992	EF-hand-dom_pair	Homologous_superfamily
IPR018247	EF_Hand_1_Ca_BS	Binding_site

Pfam: PF13499

UniProt features (36 total): sequence variant 9, binding site 5, domain 4, coiled-coil region 4, region of interest 3, short sequence motif 2, compositionally biased region 2, mutagenesis site 2, sequence conflict 2, chain 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y2I6-F1	66.82	0.29

Functional residue map

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

Ligand- & substrate-binding residues (5): 246; 248; 250; 252; 257

Post-translational modifications (1): 148

Mutagenesis-validated functional residues (2):

Position	Phenotype
495–497	disrupts binding to cdc20 and fzr1 and prevents ubiquitination and subsequent degradation of ninl; when associated with
633–636	disrupts binding to cdc20 and fzr1 and prevents ubiquitination and subsequent degradation of ninl; when associated with

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

ID	Pathway
R-HSA-2565942	Regulation of PLK1 Activity at G2/M Transition
R-HSA-380259	Loss of Nlp from mitotic centrosomes
R-HSA-380270	Recruitment of mitotic centrosome proteins and complexes
R-HSA-380284	Loss of proteins required for interphase microtubule organization from the centrosome
R-HSA-380320	Recruitment of NuMA to mitotic centrosomes
R-HSA-5620912	Anchoring of the basal body to the plasma membrane
R-HSA-8854518	AURKA Activation by TPX2

MSigDB gene sets: 109 (showing top): GOBP_MICROTUBULE_ANCHORING, IVANOVA_HEMATOPOIESIS_MATURE_CELL, GOCC_MICROTUBULE_ORGANIZING_CENTER, PID_PLK1_PATHWAY, GOCC_CENTROSOME, ALCALA_APOPTOSIS, LEE_RECENT_THYMIC_EMIGRANT, SANSOM_APC_TARGETS, chr20p11, ACACTGG_MIR199A_MIR199B, GOBP_MICROTUBULE_CYTOSKELETON_ORGANIZATION, FEVR_CTNNB1_TARGETS_DN, GOBP_MICROTUBULE_ANCHORING_AT_MICROTUBULE_ORGANIZING_CENTER, ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN, GOCC_SUPRAMOLECULAR_COMPLEX

GO Biological Process (1): microtubule anchoring at centrosome (GO:0034454)

GO Molecular Function (3): calcium ion binding (GO:0005509), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (6): centrosome (GO:0005813), cytosol (GO:0005829), microtubule (GO:0005874), cytoplasm (GO:0005737), microtubule organizing center (GO:0005815), cytoskeleton (GO:0005856)

Reactome top-level categories

Rollup of top-5 pathways:

Category	Pathways
G2/M Transition	2
Centrosome maturation	2
Loss of proteins required for interphase microtubule organization from the centrosome	1
Mitotic Prometaphase	1
Assembly of the 9+0 primary cilium	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
microtubule cytoskeleton	2
microtubule anchoring at microtubule organizing center	1
metal ion binding	1
binding	1
cation binding	1
centriole	1
microtubule organizing center	1
cytoplasm	1
polymeric cytoskeletal fiber	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1382 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NINL	LCA5	Q86VQ0	924
NINL	USH2A	O75445	899
NINL	BICDL1	Q6ZP65	761
NINL	TUBG1	P23258	711
NINL	HOOK3	Q86VS8	695
NINL	BICD2	Q8TD16	659
NINL	HOOK1	Q9UJC3	659
NINL	CNTRL	Q7Z7A1	625
NINL	WHRN	Q9P202	620
NINL	OFD1	O75665	608
NINL	PLK1	P53350	599
NINL	TUBGCP4	Q9UGJ1	596
NINL	RAB11FIP3	O75154	588
NINL	DCTN1	Q14203	582
NINL	CEP192	Q8TEP8	569

IntAct

104 interactions, top by confidence:

A	B	Type	Score
ZNF417	NINL	psi-mi:“MI:0915”(physical association)	0.670
RCOR3	NINL	psi-mi:“MI:0915”(physical association)	0.670
NINL	RCOR3	psi-mi:“MI:0915”(physical association)	0.670
FAM9C	NDC80	psi-mi:“MI:0914”(association)	0.670
FAM161A	NINL	psi-mi:“MI:0915”(physical association)	0.560
CCDC146	NINL	psi-mi:“MI:0915”(physical association)	0.560
NINL	L3MBTL4	psi-mi:“MI:0915”(physical association)	0.560
CCHCR1	NINL	psi-mi:“MI:0915”(physical association)	0.560
NINL	KAT5	psi-mi:“MI:0915”(physical association)	0.560
NINL	HAUS1	psi-mi:“MI:0915”(physical association)	0.560
RBM41	NINL	psi-mi:“MI:0915”(physical association)	0.560
SH2D4A	NINL	psi-mi:“MI:0915”(physical association)	0.560
NINL	CCDC146	psi-mi:“MI:0915”(physical association)	0.560
L3MBTL4	NINL	psi-mi:“MI:0915”(physical association)	0.560
NINL	CCHCR1	psi-mi:“MI:0915”(physical association)	0.560
HAUS1	NINL	psi-mi:“MI:0915”(physical association)	0.560
NINL	RBM41	psi-mi:“MI:0915”(physical association)	0.560
NINL	FAM161A	psi-mi:“MI:0915”(physical association)	0.560
KAT5	NINL	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (578): NINL (Two-hybrid), CCHCR1 (Two-hybrid), RBM41 (Two-hybrid), RCOR3 (Two-hybrid), CCDC146 (Two-hybrid), SH2D4A (Two-hybrid), FAM161A (Two-hybrid), L3MBTL4 (Two-hybrid), HAUS1 (Two-hybrid), ZNF417 (Two-hybrid), NINL (Affinity Capture-MS), SPERT (Two-hybrid), NINL (Two-hybrid), CCDC33 (Two-hybrid), NINL (Two-hybrid)

ESM2 similar proteins: A0A0J9YX94, A0A0J9YXQ4, A0A0J9YY54, A0A494C1R9, A5D7L8, A6NDY0, A6NKD2, A7E321, E9PGG2, F6SZT2, O14771, O19110, O75807, O88852, P0CV98, P0CV99, P0CW00, P0CW01, P0CW24, P17564, P78358, Q01534, Q0P5N2, Q15735, Q2KI51, Q2M329, Q587J8, Q5DTT8, Q5R5G8, Q5R6R8, Q5SV97, Q60465, Q62881, Q69ZB3, Q6P752, Q86V59, Q8BSI6, Q8IWY8, Q8N3D4, Q8VD63

Diamond homologs: G9G127, Q61043, Q6ZQ12, Q8N4C6, Q9Y2I6, A7K6Y8, A7K6Y9, O77691, O77791, P02632, P02633, P02634, P02638, P02639, P04163, P04271, P04631, P05109, P05942, P05943, P05964, P06702, P06703, P07091, P08207, P10462, P14069, P20930, P22793, P23297, P24479, P24480, P25815, P26447, P27003, P28318, P28782, P28783, P29034, P29377

SIGNOR signaling

9 interactions.

A	Effect	B	Mechanism
AURKB	up-regulates	NINL	phosphorylation
CDK1	“up-regulates activity”	NINL	phosphorylation
CDK1	“down-regulates quantity by destabilization”	NINL	phosphorylation
PLK1	“down-regulates activity”	NINL	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 90 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
Loss of Nlp from mitotic centrosomes	5	16.2×	1e-03
Loss of proteins required for interphase microtubule organization from the centrosome	5	16.2×	1e-03
AURKA Activation by TPX2	5	15.5×	1e-03
Recruitment of mitotic centrosome proteins and complexes	5	13.9×	2e-03
Anchoring of the basal body to the plasma membrane	6	13.8×	1e-03
Regulation of PLK1 Activity at G2/M Transition	5	12.9×	2e-03
Recruitment of NuMA to mitotic centrosomes	5	11.9×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
cilium assembly	9	8.5×	6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	208
Likely benign	33
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

6483 predictions. Top by Δscore:

Variant	Effect	Δscore
20:25453638:TCAAA:T	acceptor_gain	1.0000
20:25453639:CAAA:C	acceptor_gain	1.0000
20:25453639:CAAAC:C	acceptor_gain	1.0000
20:25453640:AAA:A	acceptor_gain	1.0000
20:25453641:AA:A	acceptor_gain	1.0000
20:25453642:AC:A	acceptor_loss	1.0000
20:25453643:C:CC	acceptor_gain	1.0000
20:25455669:TCA:T	donor_loss	1.0000
20:25455670:CACCT:C	donor_loss	1.0000
20:25455671:A:AC	donor_gain	1.0000
20:25455671:ACCTG:A	donor_gain	1.0000
20:25455672:C:CT	donor_gain	1.0000
20:25455672:CCTG:C	donor_gain	1.0000
20:25455672:CCTGC:C	donor_gain	1.0000
20:25455786:CCTGC:C	acceptor_loss	1.0000
20:25455788:T:A	acceptor_loss	1.0000
20:25455791:C:CT	acceptor_gain	1.0000
20:25455791:C:T	acceptor_gain	1.0000
20:25458377:ACTT:A	donor_loss	1.0000
20:25458378:CTTA:C	donor_loss	1.0000
20:25458379:TTACC:T	donor_loss	1.0000
20:25458380:TACCC:T	donor_loss	1.0000
20:25458381:A:AT	donor_loss	1.0000
20:25458381:AC:A	donor_gain	1.0000
20:25458382:CC:C	donor_gain	1.0000
20:25458382:CCCG:C	donor_gain	1.0000
20:25469985:CCTTA:C	donor_loss	1.0000
20:25469987:TTAC:T	donor_loss	1.0000
20:25469988:TACC:T	donor_loss	1.0000
20:25469989:A:AC	donor_gain	1.0000

AlphaMissense

9018 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:25500881:A:G	W331R	0.994
20:25500881:A:T	W331R	0.994
20:25489972:A:G	L500P	0.989
20:25498303:A:G	L359P	0.988
20:25517833:A:G	F66S	0.987
20:25526493:A:G	L32P	0.985
20:25517829:C:A	K67N	0.983
20:25517829:C:G	K67N	0.983
20:25498335:G:C	F348L	0.979
20:25498335:G:T	F348L	0.979
20:25498337:A:G	F348L	0.979
20:25517832:A:C	F66L	0.979
20:25517832:A:T	F66L	0.979
20:25517834:A:G	F66L	0.979
20:25482075:A:G	L568P	0.978
20:25489909:A:G	L521P	0.978
20:25504040:A:G	F258S	0.978
20:25500844:A:G	L343S	0.977
20:25482096:A:G	L561P	0.976
20:25498295:C:G	A362P	0.976
20:25498291:A:G	L363P	0.975
20:25517841:A:C	F63L	0.974
20:25517841:A:T	F63L	0.974
20:25517843:A:G	F63L	0.974
20:25500879:C:A	W331C	0.971
20:25500879:C:G	W331C	0.971
20:25500880:C:G	W331S	0.970
20:25489897:A:G	L525P	0.969
20:25489939:A:G	L511P	0.969
20:25498303:A:T	L359Q	0.969

dbSNP variants (sampled 300 via entrez): RS1000017859 (20:25560767 C>T), RS1000040545 (20:25504520 A>T), RS1000051052 (20:25527791 TG>T,TGG), RS1000118747 (20:25528769 A>G), RS1000124468 (20:25580114 C>G,T), RS1000128040 (20:25569382 C>T), RS1000135605 (20:25574399 C>A,T), RS1000172166 (20:25466185 C>T), RS1000172962 (20:25472995 T>C), RS1000176653 (20:25500404 G>A,T), RS1000244938 (20:25484326 T>A), RS1000252012 (20:25543638 C>T), RS1000261440 (20:25561422 G>C), RS1000275280 (20:25532895 C>T), RS1000321694 (20:25574157 T>A)

Disease associations

OMIM: gene MIM:609580 | 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

5 associations (top):

Study	Trait	p-value
GCST006485_14	Telomere length	2.000000e-06
GCST006976_138	Macular thickness	5.000000e-08
GCST008971_104	Urate levels	2.000000e-06
GCST008972_245	Urate levels	3.000000e-09
GCST010703_48	Brain morphology (MOSTest)	1.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004531	urate measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	4
Valproic Acid	affects expression, decreases expression, increases methylation	4
Aflatoxin B1	decreases methylation, decreases expression	4
lasiocarpine	decreases expression	2
methyleugenol	decreases expression	2
bisphenol S	affects cotreatment, increases methylation, decreases expression	2
N-Nitrosopyrrolidine	decreases expression	2
Nickel	decreases expression	2
Tobacco Smoke Pollution	decreases expression	2
GSK-J4	decreases expression	1
bisphenol F	affects cotreatment, decreases expression	1
triphenyl phosphate	affects expression	1
cinnamaldehyde	increases expression	1
beta-lapachone	decreases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	decreases expression	1
benzo(e)pyrene	increases methylation	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
nickel sulfate	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1
K 7174	increases expression	1
clothianidin	decreases expression	1
jinfukang	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Resveratrol	decreases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Leflunomide	decreases expression	1
Cadmium	decreases expression, increases abundance	1
Coumestrol	affects cotreatment, 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