RRN3

Summary

RRN3 (RNA polymerase I transcription factor RRN3, HGNC:30346) is a protein-coding gene on chromosome 16p13.11, encoding RNA polymerase I-specific transcription initiation factor RRN3 (Q9NYV6). Required for efficient transcription initiation by RNA polymerase I (Pol I). It is a common-essential gene (DepMap: required in 100.0% of cancer cell lines).

Enables RNA polymerase I core promoter sequence-specific DNA binding activity and RNA polymerase I general transcription initiation factor activity. Involved in transcription initiation at RNA polymerase I promoter. Located in nucleolus.

Source: NCBI Gene 54700 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 4 total
• Cancer driver (intOGen): activating (oncogene-like) across 1 cancer types
• Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_018427

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30346
Approved symbol	RRN3
Name	RNA polymerase I transcription factor RRN3
Location	16p13.11
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp566E104, TIF-IA
Ensembl gene	ENSG00000085721
Ensembl biotype	protein_coding
OMIM	605121
Entrez	54700

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 retained_intron

ENST00000198767, ENST00000327307, ENST00000429751, ENST00000561685, ENST00000563559, ENST00000564131, ENST00000874881, ENST00000874882

RefSeq mRNA: 2 — MANE Select: NM_018427 NM_001301064, NM_018427

CCDS: CCDS10559, CCDS73833

Canonical transcript exons

ENST00000198767 — 18 exons

Exon	Start	End
ENSE00000670606	15084642	15084705
ENSE00000670612	15074723	15074861
ENSE00001321030	15072950	15073080
ENSE00001593525	15071121	15071251
ENSE00001594015	15085639	15085698
ENSE00001599371	15083513	15083582
ENSE00001613910	15070070	15070254
ENSE00001648230	15068169	15068277
ENSE00001663139	15065219	15065371
ENSE00001695252	15086365	15086454
ENSE00001729849	15091315	15091371
ENSE00001737475	15063196	15063283
ENSE00001869221	15060033	15061905
ENSE00002616919	15094145	15094272
ENSE00003544327	15086129	15086258
ENSE00003544685	15076558	15076650
ENSE00003574677	15079998	15080096
ENSE00003590338	15092509	15092614

Expression profiles

Bgee: expression breadth ubiquitous, 142 present calls, max score 94.60.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	94.60	gold quality
calcaneal tendon	UBERON:0003701	93.27	gold quality
ganglionic eminence	UBERON:0004023	92.50	gold quality
embryo	UBERON:0000922	92.49	gold quality
gastrocnemius	UBERON:0001388	92.24	gold quality
muscle of leg	UBERON:0001383	91.93	gold quality
skeletal muscle organ	UBERON:0014892	91.84	gold quality
ventricular zone	UBERON:0003053	91.14	gold quality
endometrium	UBERON:0001295	91.09	gold quality
islet of Langerhans	UBERON:0000006	90.80	gold quality
rectum	UBERON:0001052	90.31	gold quality
adrenal tissue	UBERON:0018303	89.99	gold quality
subcutaneous adipose tissue	UBERON:0002190	89.80	gold quality
ovary	UBERON:0000992	89.61	gold quality
hindlimb stylopod muscle	UBERON:0004252	89.61	gold quality
skeletal muscle tissue	UBERON:0001134	89.58	gold quality
right ovary	UBERON:0002118	89.55	gold quality
adipose tissue	UBERON:0001013	89.49	gold quality
left ovary	UBERON:0002119	89.46	gold quality
lymph node	UBERON:0000029	89.36	gold quality
omental fat pad	UBERON:0010414	89.11	gold quality
smooth muscle tissue	UBERON:0001135	88.98	gold quality
muscle tissue	UBERON:0002385	88.85	gold quality
mammary gland	UBERON:0001911	88.77	gold quality
thoracic mammary gland	UBERON:0005200	88.77	gold quality
left uterine tube	UBERON:0001303	88.76	gold quality
fallopian tube	UBERON:0003889	88.64	gold quality
uterus	UBERON:0000995	88.59	gold quality
right lobe of liver	UBERON:0001114	88.53	gold quality
nerve	UBERON:0001021	88.22	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.71

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): GLI3, SSRP1

miRNA regulators (miRDB)

88 targeting RRN3, 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-3613-3P	100.00	76.36	7965
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-320A-3P	99.77	69.73	2107
HSA-MIR-320B	99.77	69.73	2107
HSA-MIR-320C	99.77	69.73	2107
HSA-MIR-320D	99.77	69.73	2107

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 11)

• Data show that nutrient starvation, density arrest and protein synthesis inhibitors inactivate transcription initiation factor-IA and impair its association with RNA polymerase I. (PMID:12393749)
• ERK-dependent phosphorylation of the transcription initiation factor TIF-IA is required for RNA polymerase I transcription and cell growth. (PMID:12620228)
• Phosphorylation of S44 activates and S199 inactivates TIF-IA. (PMID:15004009)
• The definition of the Alu element within the TIF-IA gene as an exon is restricted to certain types of cancers; the element is not exonized in normal human cells. (PMID:18047649)
• CK2 phosphorylates the transcription initiation factor TIF-IA at serines 170 and 172 (Ser170/172), and this phosphorylation triggers the release of TIF-IA from Pol I after transcription initiation. (PMID:18559419)
• reveals the molecular basis of Rrn3-regulated Pol I initiation and cell growth (PMID:21940764)
• DNA binding by the ribosomal DNA transcription factor rrn3 is essential for ribosomal DNA transcription (PMID:23393135)
• These data support a model in which activated Akt enhances rRNA synthesis both by preventing TIF-IA degradation and phosphorylating CK2alpha, which in turn phosphorylates TIF-IA. (PMID:24297901)
• Specific stress stimuli of NF-kappaB induce degradation of a critical component of the PolI complex, TIF-IA. This degradation precedes activation of NF-kappaB and is associated with increased nucleolar size. (PMID:29873780)
• Depletion of Ebp1 expression in primary colon cancer cells inhibits cell proliferation, colony forming, and invasion in vitro as well as tumor formation in vivo and enhances cell sensitivity to irradiation. We further demonstrated that Ebp1 interacts with TIF-90, a splice variant of transcription initiation factor IA (TIF-IA) of the RNA polymerase I complex. (PMID:30793766)
• High RRN3 expression is associated with malignant characteristics and poor prognosis in pancreatic cancer. (PMID:37119370)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	rrn3	ENSDARG00000102997
mus_musculus	Rrn3	ENSMUSG00000022682
rattus_norvegicus	Rrn3	ENSRNOG00000003326
drosophila_melanogaster	Tif-IA	FBGN0032988
caenorhabditis_elegans		WBGENE00007980

Protein

Protein identifiers

RNA polymerase I-specific transcription initiation factor RRN3 — Q9NYV6 (reviewed: Q9NYV6)

Alternative names: Transcription initiation factor IA

All UniProt accessions (3): Q9NYV6, F5H148, H3BMT1

UniProt curated annotations — full annotation on UniProt →

Function. Required for efficient transcription initiation by RNA polymerase I (Pol I). Required for the formation of the competent pre-initiation complex (PIC).

Subunit / interactions. Part of Pol I pre-initiation complex (PIC), in which Pol I core assembles with RRN3 and promoter-bound UTBF and SL1/TIF-IB complex. Interacts with POLR1F, EIF3L, TAF1B and TAF1C.

Subcellular location. Nucleus. Nucleolus.

Post-translational modifications. Phosphorylation is required for participation in rDNA transcription. Phosphorylated at Thr-200 by MAPK9/JNK2, which abrogates initiation complex formation.

Similarity. Belongs to the RRN3 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9NYV6-1	1	yes
Q9NYV6-2	2
Q9NYV6-3	3
Q9NYV6-4	4

RefSeq proteins (2): NP_001287993, NP_060897* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007991	RNA_pol_I_trans_ini_fac_RRN3	Family

Pfam: PF05327

UniProt features (43 total): helix 21, splice variant 5, turn 4, modified residue 4, region of interest 3, strand 2, chain 1, sequence variant 1, mutagenesis site 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
7OBA	ELECTRON MICROSCOPY	3.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NYV6-F1	78.36	0.59

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 (4): 170, 172, 200, 640

Mutagenesis-validated functional residues (1):

Position	Phenotype
411–415	abolishes interaction with taf1b and taf1c.

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-73762	RNA Polymerase I Transcription Initiation
R-HSA-73772	RNA Polymerase I Promoter Escape
R-HSA-73854	RNA Polymerase I Promoter Clearance
R-HSA-73864	RNA Polymerase I Transcription
R-HSA-74160	Gene expression (Transcription)

MSigDB gene sets: 175 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_NEGATIVE_REGULATION_OF_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_BY_P53_CLASS_MEDIATOR, REACTOME_RNA_POLYMERASE_I_TRANSCRIPTION_INITIATION, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, PID_MTOR_4PATHWAY, GOBP_NEGATIVE_REGULATION_OF_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, ONKEN_UVEAL_MELANOMA_UP, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT, GOBP_APOPTOTIC_SIGNALING_PATHWAY, WANG_LMO4_TARGETS_DN, MARTINEZ_RB1_TARGETS_DN, GOBP_NUCLEUS_ORGANIZATION, GOBP_REGULATION_OF_DNA_TEMPLATED_TRANSCRIPTION_INITIATION, GOBP_DNA_TEMPLATED_TRANSCRIPTION_INITIATION

GO Biological Process (13): in utero embryonic development (GO:0001701), transcription initiation at RNA polymerase I promoter (GO:0006361), nucleolus organization (GO:0007000), cytoplasm organization (GO:0007028), ribosome biogenesis (GO:0042254), positive regulation of DNA-templated transcription (GO:0045893), fibroblast proliferation (GO:0048144), homeostasis of number of cells (GO:0048872), intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332), negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254), regulation of DNA-templated transcription initiation (GO:2000142), RNA polymerase I preinitiation complex assembly (GO:0001188), DNA-templated transcription initiation (GO:0006352)

GO Molecular Function (5): RNA polymerase I core binding (GO:0001042), RNA polymerase I core promoter sequence-specific DNA binding (GO:0001164), RNA polymerase I general transcription initiation factor activity (GO:0001181), protein binding (GO:0005515), RNA polymerase binding (GO:0070063)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
RNA Polymerase I Promoter Clearance	2
RNA Polymerase I Transcription	1
Gene expression (Transcription)	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription initiation	2
transcription by RNA polymerase I	2
DNA-templated transcription	2
regulation of DNA-templated transcription	2
nuclear lumen	2
chordate embryonic development	1
nucleus organization	1
cellular component organization	1
ribonucleoprotein complex biogenesis	1
positive regulation of RNA biosynthetic process	1
cell population proliferation	1
multicellular organismal-level homeostasis	1
signal transduction by p53 class mediator	1
intrinsic apoptotic signaling pathway	1
intrinsic apoptotic signaling pathway by p53 class mediator	1
negative regulation of signal transduction by p53 class mediator	1
regulation of intrinsic apoptotic signaling pathway by p53 class mediator	1
negative regulation of intrinsic apoptotic signaling pathway	1
transcription initiation at RNA polymerase I promoter	1
transcription preinitiation complex assembly	1
RNA biosynthetic process	1
RNA polymerase core enzyme binding	1
core promoter sequence-specific DNA binding	1
RNA polymerase I transcription regulatory region sequence-specific DNA binding	1
RNA polymerase I preinitiation complex assembly	1
general transcription initiation factor activity	1
binding	1
enzyme binding	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1354 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RRN3	POLI	Q9UNA4	997
RRN3	UBTF	P17480	934
RRN3	TBP	P20226	926
RRN3	POLR1C	O15160	880
RRN3	TAF1C	Q15572	878
RRN3	TAF1A	Q15573	870
RRN3	POLR1G	O15446	854
RRN3	POLR1B	Q9H9Y6	831
RRN3	POLR1F	Q3B726	807
RRN3	TAF1B	Q53T94	795
RRN3	POLR1E	Q9GZS1	795
RRN3	POLR1A	O95602	744
RRN3	TRIM28	Q13263	743
RRN3	POLR1H	Q9P1U0	716
RRN3	PDXDC1	Q6P996	710

IntAct

24 interactions, top by confidence:

A	B	Type	Score
POLR2L	RCCD1	psi-mi:“MI:0914”(association)	0.640
POLR2F	POLR3A	psi-mi:“MI:0914”(association)	0.640
POLR1F	POLR1A	psi-mi:“MI:0914”(association)	0.640
POLR2L	POLR3A	psi-mi:“MI:0914”(association)	0.640
IL17RD	RRN3	psi-mi:“MI:0915”(physical association)	0.560
TMEM108	TCAF2	psi-mi:“MI:0914”(association)	0.530
POLR1C	POLR3A	psi-mi:“MI:0914”(association)	0.530
RRN3	POLR1A	psi-mi:“MI:0914”(association)	0.530
SET	RRN3	psi-mi:“MI:0915”(physical association)	0.400
POLR1C	POLR3A	psi-mi:“MI:0914”(association)	0.350
POLR1F	POLR1C	psi-mi:“MI:0914”(association)	0.350
TAF1D		psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
NPTN	RTL8C	psi-mi:“MI:0914”(association)	0.350
POLR1D	POLR3A	psi-mi:“MI:0914”(association)	0.350
POLR1H	POLR1C	psi-mi:“MI:0914”(association)	0.350
RRN3	POLR1G	psi-mi:“MI:0914”(association)	0.350
POLR1D	RPSA2	psi-mi:“MI:0914”(association)	0.350

BioGRID (61): RPA43 (Affinity Capture-Western), TAF12 (Affinity Capture-Western), RRN3 (Affinity Capture-MS), RRN3 (Affinity Capture-RNA), MYO1C (Affinity Capture-Western), RRN3 (Affinity Capture-Western), RRN3 (Affinity Capture-MS), RRN3 (Affinity Capture-MS), RRN3 (Affinity Capture-MS), RRN3 (Affinity Capture-MS), RRN3 (Affinity Capture-MS), PA2G4 (Affinity Capture-Western), Polr1b (Affinity Capture-Western), RRN3 (Reconstituted Complex), RRN3 (Reconstituted Complex)

ESM2 similar proteins: A0A571BF63, A0JMA8, A1A535, A1A5P5, A1ZBE8, A6H8H2, A8XSV3, B0BF33, B2RS91, E7F187, O17237, O43150, P25054, P30630, Q05B30, Q09263, Q14156, Q14738, Q14D04, Q19317, Q1AAU6, Q21106, Q2KI89, Q5PQS3, Q5R4N9, Q5R629, Q5RAY1, Q5SPP5, Q5U245, Q5VZ89, Q61315, Q61QK6, Q620W3, Q641A2, Q6ZQ18, Q7SIG6, Q7Z3E5, Q7Z401, Q7Z7A4, Q8BG67

Diamond homologs: A6NIE6, B2RS91, Q2M238, Q5R4N9, Q9NYV6, P36070, P48322, Q10110

SIGNOR signaling

11 interactions.

A	Effect	B	Mechanism
CDK2	up-regulates	RRN3	phosphorylation
MAPK9	down-regulates	RRN3	phosphorylation
CSNK2A1	down-regulates	RRN3	phosphorylation
PRKAA1	down-regulates	RRN3	phosphorylation
AMPK	down-regulates	RRN3	phosphorylation
CyclinE/CDK2	up-regulates	RRN3	phosphorylation
RRN3	“up-regulates activity”	“SL1 complex”	relocalization
RRN3	“up-regulates activity”	“RNA Polymerase I”	relocalization
MAPK3	up-regulates	RRN3	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 19 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
RNA Polymerase III Chain Elongation	5	226.6×	1e-10
Positive epigenetic regulation of rRNA expression	9	222.5×	8e-19
RNA Polymerase I Transcription Termination	9	209.8×	8e-19
RNA Polymerase I Promoter Clearance	9	188.2×	2e-18
RNA Polymerase I Transcription	9	183.5×	2e-18
RNA Polymerase III Transcription Termination	5	177.3×	4e-10
Negative epigenetic regulation of rRNA expression	9	166.8×	3e-18
RNA Polymerase III Transcription Initiation From Type 2 Promoter	5	151.1×	8e-10

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 1 cancer types — COADREAD.

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

2367 predictions. Top by Δscore:

Variant	Effect	Δscore
16:15061902:TGTC:T	acceptor_gain	1.0000
16:15061904:TCCTG:T	acceptor_loss	1.0000
16:15061905:CCT:C	acceptor_loss	1.0000
16:15061906:C:CC	acceptor_gain	1.0000
16:15061906:CTGC:C	acceptor_loss	1.0000
16:15063192:TGAC:T	donor_loss	1.0000
16:15063193:GACCT:G	donor_loss	1.0000
16:15063194:ACCTT:A	donor_loss	1.0000
16:15063195:C:A	donor_loss	1.0000
16:15065216:TA:T	donor_loss	1.0000
16:15065217:A:AC	donor_gain	1.0000
16:15065218:C:CC	donor_gain	1.0000
16:15065218:CCT:C	donor_gain	1.0000
16:15065368:CTTA:C	acceptor_gain	1.0000
16:15065369:TTA:T	acceptor_gain	1.0000
16:15065370:TA:T	acceptor_gain	1.0000
16:15065372:C:CC	acceptor_gain	1.0000
16:15065372:C:T	acceptor_loss	1.0000
16:15065373:T:A	acceptor_loss	1.0000
16:15065374:G:GC	acceptor_gain	1.0000
16:15065380:C:CT	acceptor_gain	1.0000
16:15065381:A:T	acceptor_gain	1.0000
16:15068163:ACTT:A	donor_loss	1.0000
16:15068164:CTT:C	donor_loss	1.0000
16:15068165:TTAC:T	donor_loss	1.0000
16:15068166:TAC:T	donor_loss	1.0000
16:15068167:A:AC	donor_gain	1.0000
16:15068168:C:CC	donor_gain	1.0000
16:15068168:CT:C	donor_gain	1.0000
16:15068168:CTT:C	donor_gain	1.0000

AlphaMissense

4326 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:15071153:G:C	S409R	0.999
16:15071153:G:T	S409R	0.999
16:15071155:T:G	S409R	0.999
16:15086194:A:G	L136P	0.999
16:15070136:A:G	C460R	0.998
16:15071157:C:T	G408E	0.998
16:15071223:A:G	L386P	0.998
16:15083568:A:G	L204P	0.998
16:15084679:G:C	H187D	0.998
16:15086158:A:G	L148P	0.998
16:15086249:A:G	W118R	0.998
16:15086249:A:T	W118R	0.998
16:15086432:A:G	L92P	0.998
16:15092548:A:C	F52L	0.998
16:15092548:A:T	F52L	0.998
16:15092550:A:G	F52L	0.998
16:15065239:A:C	F562L	0.997
16:15065239:A:T	F562L	0.997
16:15065241:A:G	F562L	0.997
16:15071139:G:T	A414D	0.997
16:15071140:C:G	A414P	0.997
16:15071142:C:A	R413I	0.997
16:15071145:G:T	A412E	0.997
16:15071158:C:G	G408R	0.997
16:15071158:C:T	G408R	0.997
16:15072964:A:G	C372R	0.997
16:15074779:A:G	L314P	0.997
16:15080074:A:G	L230P	0.997
16:15080079:G:C	N228K	0.997
16:15080079:G:T	N228K	0.997

dbSNP variants (sampled 300 via entrez): RS1000050810 (16:15087395 C>A,G), RS1000321322 (16:15082206 T>C), RS1000454839 (16:15072688 C>A,G,T), RS1000569367 (16:15066929 G>A), RS1000589940 (16:15072554 C>T), RS1000652440 (16:15087512 C>A,G), RS1000825501 (16:15090875 T>G), RS1001171493 (16:15067248 T>C), RS1001182402 (16:15081234 A>C), RS1001252655 (16:15086360 C>T), RS1001318363 (16:15080986 TTCATA>T), RS1001406060 (16:15072281 C>A), RS1001449505 (16:15071682 C>G,T), RS1001583962 (16:15071467 A>G), RS1001774967 (16:15065887 A>C)

Disease associations

OMIM: gene MIM:605121 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST002444_7	Plasma omega-6 polyunsaturated fatty acid levels (dihomo-gamma-linolenic acid)	2.000000e-67
GCST002444_8	Plasma omega-6 polyunsaturated fatty acid levels (dihomo-gamma-linolenic acid)	5.000000e-25
GCST002446_5	Plasma omega-6 polyunsaturated fatty acid levels (linoleic acid)	1.000000e-15
GCST002446_8	Plasma omega-6 polyunsaturated fatty acid levels (linoleic acid)	4.000000e-14
GCST002450_10	Plasma omega-6 polyunsaturated fatty acid levels (gamma-linolenic acid)	2.000000e-12
GCST008595_202	Cognitive ability, years of educational attainment or schizophrenia (pleiotropy)	6.000000e-11
GCST010136_16	Fruit consumption	2.000000e-08
GCST010173_22	Triglyceride levels	1.000000e-20
GCST012020_126	Serum metabolite levels	7.000000e-11

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0005680	omega-6 polyunsaturated fatty acid measurement
EFO:0004337	intelligence
EFO:0004784	self reported educational attainment
EFO:0008111	diet measurement
EFO:0004530	triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Cadmium Chloride	increases expression, decreases expression, increases methylation, increases abundance	3
sodium arsenite	affects cotreatment, increases abundance, increases expression	2
Arsenic	affects methylation, affects cotreatment, increases abundance, increases expression	2
Tobacco Smoke Pollution	increases expression	2
Valproic Acid	affects expression, decreases expression	2
FR900359	decreases phosphorylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, increases activity, increases expression	1
arsenite	affects binding, decreases reaction	1
butyraldehyde	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
coumarin	increases phosphorylation	1
perfluoro-n-nonanoic acid	increases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
1-(4-(6-bromobenzo(1,3)dioxol-5-yl)-3a,4,5,9b-tetrahydro-3H-cyclopenta(c)quinolin-8-yl)ethanone	decreases phosphorylation	1
jinfukang	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases abundance, increases expression	1
Cisplatin	decreases expression, affects cotreatment	1
Estradiol	decreases phosphorylation	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1

Clinical trials (associated diseases)

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