USP6NL

Summary

USP6NL (USP6 N-terminal like, HGNC:16858) is a protein-coding gene on chromosome 10p14, encoding USP6 N-terminal-like protein (Q92738). Acts as a GTPase-activating protein for RAB43, RAB5A and RAB30.

Enables GTPase activator activity and small GTPase binding activity. Involved in several processes, including plasma membrane to endosome transport; positive regulation of GTPase activity; and retrograde transport, plasma membrane to Golgi. Located in cytoplasmic vesicle and plasma membrane.

Source: NCBI Gene 9712 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 171 total
• MANE Select transcript: NM_014688

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16858
Approved symbol	USP6NL
Name	USP6 N-terminal like
Location	10p14
Locus type	gene with protein product
Status	Approved
Aliases	RNTRE, KIAA0019, TRE2NL, RN-tre
Ensembl gene	ENSG00000148429
Ensembl biotype	protein_coding
OMIM	605405
Entrez	9712

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000277575, ENST00000379237, ENST00000443016, ENST00000606752, ENST00000609104, ENST00000609853, ENST00000938638, ENST00000938639, ENST00000938640, ENST00000938641

RefSeq mRNA: 5 — MANE Select: NM_014688 NM_001080491, NM_001391959, NM_001391960, NM_001391961, NM_014688

CCDS: CCDS44357, CCDS53492, CCDS91212

Canonical transcript exons

ENST00000609104 — 15 exons

Exon	Start	End
ENSE00000985237	11525386	11525468
ENSE00000985239	11509595	11509675
ENSE00000985240	11501101	11501208
ENSE00000999688	11485817	11485911
ENSE00000999689	11518535	11518574
ENSE00000999691	11489102	11489222
ENSE00000999693	11485169	11485234
ENSE00000999694	11490832	11490880
ENSE00000999695	11493119	11493228
ENSE00000999696	11484971	11485070
ENSE00001094541	11481770	11481922
ENSE00001166660	11527500	11527567
ENSE00001202147	11460510	11463849
ENSE00001480257	11611443	11611650
ENSE00002433384	11597631	11597717

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 96.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.3170 / max 215.6569, expressed in 1752 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
108254	7.8750	1732
108256	1.1139	610
108255	0.1935	71
108253	0.1346	36

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
amniotic fluid	UBERON:0000173	96.03	gold quality
cortical plate	UBERON:0005343	94.46	gold quality
lower esophagus mucosa	UBERON:0035834	94.01	gold quality
sperm	CL:0000019	92.87	gold quality
esophagus squamous epithelium	UBERON:0006920	92.50	gold quality
oral cavity	UBERON:0000167	91.04	gold quality
male germ cell	CL:0000015	90.49	gold quality
epithelium of esophagus	UBERON:0001976	90.47	gold quality
esophagus mucosa	UBERON:0002469	88.79	gold quality
squamous epithelium	UBERON:0006914	87.86	gold quality
epithelium of nasopharynx	UBERON:0001951	87.43	gold quality
tongue squamous epithelium	UBERON:0006919	85.96	gold quality
ventricular zone	UBERON:0003053	85.68	gold quality
gingiva	UBERON:0001828	85.37	gold quality
tonsil	UBERON:0002372	85.28	gold quality
gingival epithelium	UBERON:0001949	84.95	gold quality
palpebral conjunctiva	UBERON:0001812	84.30	gold quality
tibia	UBERON:0000979	83.97	gold quality
eye	UBERON:0000970	83.65	gold quality
ganglionic eminence	UBERON:0004023	83.15	gold quality
adrenal tissue	UBERON:0018303	82.64	gold quality
islet of Langerhans	UBERON:0000006	82.57	gold quality
esophagus	UBERON:0001043	82.37	gold quality
adult organism	UBERON:0007023	82.21	gold quality
testis	UBERON:0000473	82.14	gold quality
monocyte	CL:0000576	81.97	gold quality
mononuclear cell	CL:0000842	81.80	gold quality
endothelial cell	CL:0000115	81.76	gold quality
pigmented layer of retina	UBERON:0001782	81.71	gold quality
left testis	UBERON:0004533	81.70	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-6386	no	731.42
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

122 targeting USP6NL, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3613-3P	100.00	76.36	7965
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-6833-3P	100.00	70.63	3197
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548N	99.98	71.94	4170
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-767-5P	99.95	70.85	993

Literature-anchored findings (GeneRIF, showing 5)

• Rab5 signals to the actin cytoskeleton through RN-tre, a previously identified Rab5-specific GTPase-activating protein; RN-tre interacts with both F-actin and actinin-4, an F-actin bundling protein (PMID:15152255)
• RN-tre phosphorylation is critical for efficient hCdc14A association (PMID:17371873)
• Genome-wide significant (GWS) associations in single-nucleotide polymorphism (SNP)-based tests (P < 5 x 10(-8)) were identified for SNPs in PFDN1/HBEGF, USP6NL/ECHDC3, and BZRAP1-AS1. (PMID:28183528)
• Study reports that USP6NL is overexpressed in breast cancer, mainly of the basal-like/integrative cluster 10 subtype. Increased USP6NL levels were accompanied by gene amplification and were associated with worse prognosis in the METABRIC dataset. High levels of USP6NL in breast cancer cells delayed endocytosis and degradation of the EGFR, causing chronic AKT activation. (PMID:29691252)
• USP6NL mediated by LINC00689/miR-142-3p promotes the development of triple-negative breast cancer. (PMID:33054738)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	usp6nl	ENSDARG00000022187
mus_musculus	Usp6nl	ENSMUSG00000039046
rattus_norvegicus	Usp6nl	ENSRNOG00000017644

Paralogs (45): RABGAP1 (ENSG00000011454), TBC1D22A (ENSG00000054611), TBC1D22B (ENSG00000065491), TBC1D1 (ENSG00000065882), EVI5 (ENSG00000067208), TBC1D25 (ENSG00000068354), TBC1D2 (ENSG00000095383), TBC1D10A (ENSG00000099992), SGSM3 (ENSG00000100359), TBC1D17 (ENSG00000104946), TBC1D13 (ENSG00000107021), TBC1D12 (ENSG00000108239), TBC1D9 (ENSG00000109436), TBC1D30 (ENSG00000111490), TBC1D15 (ENSG00000121749), TBC1D5 (ENSG00000131374), TBC1D14 (ENSG00000132405), TBC1D8B (ENSG00000133138), TBC1D4 (ENSG00000136111), GRTP1 (ENSG00000139835), SGSM2 (ENSG00000141258), EVI5L (ENSG00000142459), TBCK (ENSG00000145348), RABGAP1L (ENSG00000152061), SGSM1 (ENSG00000167037), TBC1D21 (ENSG00000167139), TBC1D2B (ENSG00000167202), TBC1D16 (ENSG00000167291), TBC1D10B (ENSG00000169221), TBC1D10C (ENSG00000175463), TBC1D28 (ENSG00000189375), TBC1D9B (ENSG00000197226), TBC1D8 (ENSG00000204634), TBC1D26 (ENSG00000214946), TBC1D3G (ENSG00000260287), TBC1D3K (ENSG00000273513), TBC1D3H (ENSG00000274226), TBC1D3D (ENSG00000274419), TBC1D3L (ENSG00000274512), TBC1D3 (ENSG00000274611)

Protein

Protein identifiers

USP6 N-terminal-like protein — Q92738 (reviewed: Q92738)

Alternative names: Related to the N-terminus of tre

All UniProt accessions (3): Q92738, V9GYH2, X6RAB3

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a GTPase-activating protein for RAB43, RAB5A and RAB30. Involved in receptor trafficking. In complex with EPS8 inhibits internalization of EGFR. Involved in retrograde transport from the endocytic pathway to the Golgi apparatus. Involved in the transport of Shiga toxin from early and recycling endosomes to the trans-Golgi network. Required for structural integrity of the Golgi complex.

Subunit / interactions. Interacts with EPS8. Interacts with RAB43 and RAB30 (GTP-bound); acts as a GAP.

Subcellular location. Golgi apparatus. Cytoplasmic vesicle.

Tissue specificity. Widely expressed.

Isoforms (2)

UniProt ID	Names	Canonical?
Q92738-1	1	yes
Q92738-2	2

RefSeq proteins (5): NP_001073960, NP_001378888, NP_001378889, NP_001378890, NP_055503* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000195	Rab-GAP-TBC_dom	Domain
IPR035969	Rab-GAP_TBC_sf	Homologous_superfamily
IPR050302	Rab_GAP_TBC_domain	Family

Pfam: PF00566

UniProt features (33 total): modified residue 15, compositionally biased region 9, mutagenesis site 3, region of interest 2, chain 1, domain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
9LTP	X-RAY DIFFRACTION	2.49

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q92738-F1	63.30	0.41

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 (15): 1, 391, 396, 400, 546, 549, 582, 585, 642, 655, 659, 676, 680, 716, 729

Mutagenesis-validated functional residues (3):

Position	Phenotype
106	loss of gap activity on rab5a.
147	loss of gap activity on rab5a.
150	loss of gap activity on rab5a and rab43.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-6811440	Retrograde transport at the Trans-Golgi-Network

MSigDB gene sets: 227 (showing top): GOBP_REGULATION_OF_GOLGI_ORGANIZATION, HOEGERKORP_CD44_TARGETS_TEMPORAL_DN, GOBP_REGULATION_OF_GTPASE_ACTIVITY, BROWNE_HCMV_INFECTION_16HR_UP, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOMF_GTPASE_BINDING, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_CATALYTIC_ACTIVITY, GOBP_REGULATION_OF_HYDROLASE_ACTIVITY, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOCC_TRANS_GOLGI_NETWORK, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION, HUTTMANN_B_CLL_POOR_SURVIVAL_DN, GOBP_CILIUM_ORGANIZATION

GO Biological Process (6): Golgi organization (GO:0007030), virion assembly (GO:0019068), retrograde transport, plasma membrane to Golgi (GO:0035526), positive regulation of GTPase activity (GO:0043547), plasma membrane to endosome transport (GO:0048227), regulation of Golgi organization (GO:1903358)

GO Molecular Function (3): GTPase activator activity (GO:0005096), small GTPase binding (GO:0031267), protein binding (GO:0005515)

GO Cellular Component (5): cytosol (GO:0005829), plasma membrane (GO:0005886), cytoplasmic vesicle (GO:0031410), trans-Golgi network membrane (GO:0032588), Golgi apparatus (GO:0005794)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Intra-Golgi and retrograde Golgi-to-ER traffic	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	3
vesicle-mediated transport	2
GTPase activity	2
organelle organization	1
endomembrane system organization	1
viral process	1
viral life cycle	1
regulation of GTPase activity	1
positive regulation of hydrolase activity	1
Golgi organization	1
regulation of organelle organization	1
enzyme activator activity	1
GTPase regulator activity	1
GTPase binding	1
binding	1
cellular anatomical structure	1
membrane	1
cell periphery	1
intracellular vesicle	1
trans-Golgi network	1
organelle membrane	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

658 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
USP6NL	EPS8	Q12929	935
USP6NL	RAB5A	P20339	771
USP6NL	RAB43	Q86YS6	736
USP6NL	TRH	P20396	689
USP6NL	SOS1	Q07889	675
USP6NL	RAB11A	P24410	664
USP6NL	ABI1	Q8IZP0	615
USP6NL	ECHDC3	Q96DC8	569
USP6NL	TBC1D20	Q96BZ9	547
USP6NL	EGFR	P00533	523
USP6NL	RASA1	P20936	511
USP6NL	EGF	P01133	488
USP6NL	GRB2	P29354	481
USP6NL	ATOSB	Q7L5A3	469
USP6NL	ACTN4	O43707	453

IntAct

53 interactions, top by confidence:

A	B	Type	Score
NRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.480
Dctn3		psi-mi:“MI:0914”(association)	0.350
Map3k12	MTOR	psi-mi:“MI:0914”(association)	0.350
Ppp2ca	DKFZP586J0619	psi-mi:“MI:0914”(association)	0.350
Cenpf	WDR91	psi-mi:“MI:0914”(association)	0.350
UBE2S	RNF40	psi-mi:“MI:0914”(association)	0.350
ANAPC15		psi-mi:“MI:0914”(association)	0.350
CCNA2	ZC3H18	psi-mi:“MI:0914”(association)	0.350
Cetn2	SFI1	psi-mi:“MI:0914”(association)	0.350
COMT		psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
AXL	PIK3R2	psi-mi:“MI:0914”(association)	0.350
ARF6	USP6NL	psi-mi:“MI:0914”(association)	0.350
WWP2	CCDC85C	psi-mi:“MI:0914”(association)	0.350
FAM168A	CCDC85C	psi-mi:“MI:0914”(association)	0.350
WWC1	CIT	psi-mi:“MI:0914”(association)	0.350
USP6NL	DUSP14	psi-mi:“MI:0914”(association)	0.350
TMEM17	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
KRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
HRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
pipB2	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
CDH1	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
EGFR	FAM171A2	psi-mi:“MI:2364”(proximity)	0.270
EPHA2	ARHGAP32	psi-mi:“MI:2364”(proximity)	0.270
EPHA4	FAM171A2	psi-mi:“MI:2364”(proximity)	0.270
EPHA5	C1orf226	psi-mi:“MI:2364”(proximity)	0.270
EPHA7	PIK3R2	psi-mi:“MI:2364”(proximity)	0.270
EPHB2	ARHGAP32	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (136): USP6NL (Affinity Capture-RNA), USP6NL (Affinity Capture-RNA), USP6NL (Reconstituted Complex), USP6NL (Proximity Label-MS), USP6NL (Affinity Capture-MS), USP6NL (Affinity Capture-MS), USP6NL (Affinity Capture-MS), USP6NL (Affinity Capture-MS), USP6NL (Affinity Capture-MS), USP6NL (Affinity Capture-MS), USP6NL (Affinity Capture-MS), USP6NL (Affinity Capture-MS), USP6NL (Affinity Capture-MS), USP6NL (Proximity Label-MS), USP6NL (Affinity Capture-MS)

ESM2 similar proteins: A2VE44, A4IHD9, E6ZGB4, E7F1H9, F1QMB9, O35927, O75909, O88874, O88902, O95628, P0C090, P0CH95, P16236, P33240, P35227, P48377, P51126, Q02930, Q13191, Q3TTA7, Q4VGL6, Q5RDA3, Q5TC82, Q5XIY8, Q64213, Q6DD04, Q6DFR2, Q6NUC6, Q6NXA4, Q6NZ18, Q6NZT6, Q6PEH8, Q71SY5, Q80TJ7, Q80XC3, Q8BIQ5, Q8BT14, Q8C7E9, Q8HXM1, Q8K4S7

Diamond homologs: A0A087WVF3, A0A087WXS9, A0A087X179, A0A087X1G2, A2AWA9, A6H6A9, A6NDS4, A6NER0, B9A6J9, H2KZZ6, P0C7X1, P35125, Q2M2D7, Q5RAN1, Q5SVR0, Q66K14, Q6DHY5, Q6IPX1, Q80XC3, Q86UD7, Q8IZP1, Q92738, Q9UFV1, Q9Y3P9, A3KGB4, A6QP29, B0R0W9, B7ZAP0, O60343, O60447, O95759, O97790, P58802, P97366, Q0IIM8, Q10496, Q12317, Q12344, Q28CB1, Q3UYK3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 69 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	103.3×	1e-12
Activation of BAD and translocation to mitochondria	7	102.5×	3e-11
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	90.4×	6e-11
Activation of BH3-only proteins	7	66.8×	6e-10
RHO GTPases activate PKNs	7	42.7×	2e-08
Intrinsic Pathway for Apoptosis	7	39.4×	3e-08
FOXO-mediated transcription	5	32.3×	6e-06
Apoptosis	8	25.8×	4e-08

GO biological processes:

GO term	Partners	Fold	FDR
peptidyl-tyrosine phosphorylation	5	37.0×	7e-05
ephrin receptor signaling pathway	6	36.2×	1e-05
protein targeting	5	32.1×	8e-05
cell surface receptor protein tyrosine kinase signaling pathway	7	21.3×	2e-05
neuron apoptotic process	6	19.5×	9e-05
positive regulation of neuron projection development	6	14.4×	4e-04
MAPK cascade	5	13.4×	2e-03
intracellular protein localization	7	12.8×	1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	144
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2610 predictions. Top by Δscore:

Variant	Effect	Δscore
10:11463845:TTTAC:T	acceptor_gain	1.0000
10:11463846:TTAC:T	acceptor_gain	1.0000
10:11463847:TAC:T	acceptor_gain	1.0000
10:11463847:TACCT:T	acceptor_loss	1.0000
10:11463848:AC:A	acceptor_gain	1.0000
10:11463849:CC:C	acceptor_gain	1.0000
10:11463849:CCTGA:C	acceptor_loss	1.0000
10:11463850:C:CA	acceptor_loss	1.0000
10:11463850:C:CC	acceptor_gain	1.0000
10:11463850:C:T	acceptor_gain	1.0000
10:11481764:TCTTA:T	donor_loss	1.0000
10:11481765:CTTAC:C	donor_loss	1.0000
10:11481766:TTA:T	donor_loss	1.0000
10:11481767:TA:T	donor_loss	1.0000
10:11481768:A:AC	donor_gain	1.0000
10:11481769:C:CC	donor_gain	1.0000
10:11481769:C:CT	donor_loss	1.0000
10:11481919:TGTT:T	acceptor_gain	1.0000
10:11481920:GTT:G	acceptor_gain	1.0000
10:11481920:GTTC:G	acceptor_loss	1.0000
10:11481921:TT:T	acceptor_gain	1.0000
10:11481922:TC:T	acceptor_loss	1.0000
10:11481923:C:CC	acceptor_gain	1.0000
10:11481923:C:T	acceptor_loss	1.0000
10:11481924:T:C	acceptor_loss	1.0000
10:11481933:A:AC	acceptor_gain	1.0000
10:11481933:A:C	acceptor_gain	1.0000
10:11484969:A:AC	donor_gain	1.0000
10:11484970:C:CC	donor_gain	1.0000
10:11485003:G:C	donor_gain	1.0000

AlphaMissense

5429 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:11481802:A:G	L349P	1.000
10:11481823:A:G	L342P	1.000
10:11485043:A:G	W285R	1.000
10:11485043:A:T	W285R	1.000
10:11485195:A:G	W267R	1.000
10:11485195:A:T	W267R	1.000
10:11489147:A:G	W207R	1.000
10:11489147:A:T	W207R	1.000
10:11489148:G:C	F206L	1.000
10:11489148:G:T	F206L	1.000
10:11489149:A:G	F206S	1.000
10:11489150:A:G	F206L	1.000
10:11489176:A:G	L197P	1.000
10:11489213:A:G	Y185H	1.000
10:11490851:G:T	A175D	1.000
10:11490857:A:G	L173P	1.000
10:11490866:A:G	F170S	1.000
10:11493139:A:C	F158L	1.000
10:11493139:A:T	F158L	1.000
10:11493140:A:G	F158S	1.000
10:11493141:A:G	F158L	1.000
10:11493164:C:G	R150P	1.000
10:11493165:G:T	R150S	1.000
10:11493170:A:T	V148D	1.000
10:11493176:A:G	L146P	1.000
10:11493182:A:C	I144R	1.000
10:11493182:A:T	I144K	1.000
10:11501157:A:G	W110R	1.000
10:11501157:A:T	W110R	1.000
10:11509642:A:G	W77R	1.000

dbSNP variants (sampled 300 via entrez): RS1000001107 (10:11523802 A>G), RS1000011768 (10:11480565 C>T), RS1000019389 (10:11483130 C>T), RS1000022601 (10:11568536 T>C), RS1000045928 (10:11542271 C>T), RS1000050001 (10:11500200 A>C), RS1000064430 (10:11487802 C>A), RS1000064650 (10:11571368 A>G), RS1000126222 (10:11486269 A>C), RS1000145652 (10:11577776 C>T), RS1000148972 (10:11464026 A>G), RS1000152356 (10:11535958 T>A,C), RS1000182654 (10:11506870 C>T), RS1000189705 (10:11605774 G>A,T), RS1000217756 (10:11547925 A>C)

Disease associations

OMIM: gene MIM:605405 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001762_490	Obesity-related traits	8.000000e-06
GCST002817_12	Alzheimer’s disease in APOE e4- carriers	3.000000e-06
GCST004246_9	Alzheimer’s disease	3.000000e-08
GCST006959_73	Rheumatoid arthritis	3.000000e-07
GCST012324_13	LDL levels x SSRI defined daily dose interaction in schizophrenia or bipolar disorder	5.000000e-07

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004736	aspartate aminotransferase measurement
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0005658	response to selective serotonin reuptake inhibitor

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
Valproic Acid	affects cotreatment, increases expression, decreases methylation	8
Benzo(a)pyrene	affects methylation	2
Quercetin	decreases expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
bisphenol A	affects cotreatment, decreases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
deguelin	increases 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
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Leflunomide	increases expression	1
Caffeine	affects phosphorylation	1
Calcitriol	increases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Hydrogen Peroxide	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Tretinoin	decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases methylation	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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