TLX3

Summary

TLX3 (T cell leukemia homeobox 3, HGNC:13532) is a protein-coding gene on chromosome 5q35.1, encoding T-cell leukemia homeobox protein 3 (O43711).

The protein encoded by this gene is an orphan homeobox protein that encodes a DNA-binding nuclear transcription factor. A translocation [t(5;14)(q35;q32)] involving this gene is associated with T-cell acute lymphoblastic leukemia (T-ALL) in children and young adults.

Source: NCBI Gene 30012 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 38 total
• Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
• MANE Select transcript: NM_021025

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13532
Approved symbol	TLX3
Name	T cell leukemia homeobox 3
Location	5q35.1
Locus type	gene with protein product
Status	Approved
Aliases	RNX
Ensembl gene	ENSG00000164438
Ensembl biotype	protein_coding
OMIM	604640
Entrez	30012

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000296921

RefSeq mRNA: 1 — MANE Select: NM_021025 NM_021025

CCDS: CCDS34288

Canonical transcript exons

ENST00000296921 — 3 exons

Exon	Start	End
ENSE00001084380	171309248	171309786
ENSE00001084381	171310150	171310393
ENSE00001084382	171311389	171312139

Expression profiles

Bgee: expression breadth broad, 26 present calls, max score 82.86.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.4538 / max 483.0228, expressed in 179 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
60175	1.0202	150
60174	0.3909	125
60173	0.0427	23

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	82.86	gold quality
cerebellar cortex	UBERON:0002129	82.59	gold quality
cerebellar hemisphere	UBERON:0002245	82.59	gold quality
cerebellum	UBERON:0002037	79.80	gold quality
hair follicle	UBERON:0002073	69.43	gold quality
diaphragm	UBERON:0001103	61.33	gold quality
vena cava	UBERON:0004087	58.22	gold quality
superficial temporal artery	UBERON:0001614	54.38	gold quality
quadriceps femoris	UBERON:0001377	53.66	gold quality
vastus lateralis	UBERON:0001379	53.07	gold quality
gingival epithelium	UBERON:0001949	52.85	gold quality
deltoid	UBERON:0001476	51.49	gold quality
Brodmann (1909) area 46	UBERON:0006483	51.46	gold quality
nephron tubule	UBERON:0001231	50.73	gold quality
tibialis anterior	UBERON:0001385	50.64	silver quality
metanephric glomerulus	UBERON:0004736	49.57	gold quality
kidney epithelium	UBERON:0004819	49.35	gold quality
blood vessel layer	UBERON:0004797	49.29	gold quality
cervix squamous epithelium	UBERON:0006922	49.20	gold quality
gingiva	UBERON:0001828	49.03	gold quality
renal glomerulus	UBERON:0000074	49.02	gold quality
olfactory bulb	UBERON:0002264	48.92	gold quality
choroid plexus epithelium	UBERON:0003911	48.89	gold quality
myocardium	UBERON:0002349	48.87	gold quality
dorsal root ganglion	UBERON:0000044	48.86	gold quality
type B pancreatic cell	CL:0000169	48.83	gold quality
cardiac muscle of right atrium	UBERON:0003379	48.55	gold quality
CA1 field of hippocampus	UBERON:0003881	48.50	gold quality
left ventricle myocardium	UBERON:0006566	48.24	gold quality
orbitofrontal cortex	UBERON:0004167	48.20	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-56	yes	354.87
E-ANND-3	no	0.17

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

7 targets.

Target	Regulation
FBN1
INSR
MAP2K5
NTRK1
TH
TNFAIP8
TSC1

JASPAR motifs

Motif	Name	Family
MA2685.1	TLX3	NK

JASPAR matrix evidence (PMIDs): PMID:25428367

Upstream regulators (CollecTRI, top): HES1, PBX3, PRDM13, PTF1A, SPI1

miRNA regulators (miRDB)

23 targeting TLX3, 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-4795-3P	100.00	74.62	4024
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-7161-5P	99.68	68.92	1592
HSA-MIR-548U	99.65	67.78	1463
HSA-MIR-548AV-5P	99.60	70.84	2107
HSA-MIR-548K	99.60	70.84	2107
HSA-MIR-8054	99.48	70.81	2084
HSA-MIR-578	99.46	68.36	1787
HSA-MIR-361-3P	99.19	66.45	1381
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-4744	99.01	69.91	1581
HSA-MIR-3196	98.96	63.91	326
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-3180	98.46	64.68	348
HSA-MIR-3180-3P	98.46	64.68	348
HSA-MIR-6816-5P	98.46	64.35	364
HSA-MIR-6886-3P	96.96	66.36	844
HSA-MIR-10400-5P	96.91	66.00	56
HSA-MIR-4467	96.51	64.44	69
HSA-MIR-191-5P	95.88	67.82	171
HSA-MIR-524-3P	95.15	66.16	109
HSA-MIR-525-3P	95.15	65.95	109

Functional genomics

ClinGen dosage: haploinsufficiency 0 (no evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 20)

• HOX11L2 expression defines a clinical subtype of pediatric T-ALL associated with poor prognosis. (PMID:12130513)
• Authors conclude that RNX, and presumably its expression, are not altered in the index cases of congenital central hypoventilation syndrome. (PMID:12407709)
• High incidence of Hox11L2 expression in children with T-ALL (PMID:12454747)
• Translocations in Hox11L2 locus is associated with T-cell acute lymphoblastic leukemia (PMID:12970786)
• HOX11L2 expression is linked to chromosomes 5 and 14 in T-cell malignancies in children. (PMID:14504110)
• TLX3 expression in T-ALL is strongly associated with the presence of genomic rearrangements (PMID:15334547)
• The TLX3 protein is high levels expressed in the leukemia cells in keeping with the presence of t(5;14)(q35;q14) in leukemia cells. (PMID:15674415)
• The Significance of HOX11L2/TLX3 expression in children with T-cell acute lymphoblastic leukemia treated on Children’s Cancer Group protocols. (PMID:15990867)
• The present report is focused on the identification of elements and factors playing a role in the TLX3 physiologic expression regulation and therefore likely to be involved in cancer development. (PMID:16966433)
• In T-cell acute lymphoblastic leukemia, alternative t(5;14)(q35;q32.2) forms effect dysregulation of either TLX3 or NKX2-5 homeobox genes at 5q35 by juxtaposition with 14q32.2 breakpoints dispersed across the BCL11B downstream genomic desert. (PMID:17308084)
• five recurrent genomic deletions in TLX3 rearranged T-ALL; genome-wide overview of copy number changes in TLX3 rearranged T-ALL (PMID:18185524)
• Aberrant HOX11L2 expression is associated with thymic adult T-cell acute lymphoblastic leukemia (PMID:18368072)
• High TLX3/BCL11B fusion protein expression is associated with T/myeloid acute bilineal leukemia. (PMID:21225930)
• Results identify Tlx3 as a novel target for canonical Wnt signaling that confers somatic stem cells with a sensory neuron phenotype upon neural induction. (PMID:21374761)
• We found that 22 (21%) out of 110 clinical samples of bladder cancer showed the methylated pattern using the COBRA assay in TLX3. We found a correlation between TLX3 methylation and the sensitivity to cisplatin in the clinical samples by SDI test. (PMID:21617853)
• these results place TLX1 and TLX3 at the top of an oncogenic transcriptional network controlling leukemia development, and identify RUNX1 as a tumor-suppressor gene in T-ALL (PMID:22366949)
• The cortical thymic maturation arrest in T-lineage Acute lymphoblastic leukemias (ALLs) that overexpress TLX1 or TLX3 is due to binding of TLX1/TLX3 to ETS1. (PMID:22516263)
• Egyptian T-cell acute lymphoblastic leukemia cases seemed to have a different genetic pattern compared to other populations, with a lower incidence of TLX3/HOX11L2 and SIL/TAL but a higher incidence of NKX2-5 expression than recorded in Western countries (PMID:24571118)
• Studies suggest that homeobox protein TLX3 expression is not an indicator for the prognosis of pediatric T cell acute lymphocytic leukemia (T-ALL). (PMID:24997618)
• Immunophenotyping with CD135 and CD117 predicts the FLT3, IL-7R and TLX3 gene mutations in childhood T-cell acute leukemia. (PMID:26852660)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	tlx3b	ENSDARG00000017615
		ENSDARG00000100401
mus_musculus	Tlx3	ENSMUSG00000040610
rattus_norvegicus	Tlx3	ENSRNOG00000004976

Paralogs (42): HOXA11 (ENSG00000005073), HOXC8 (ENSG00000037965), HOXA1 (ENSG00000105991), HOXA2 (ENSG00000105996), HOXA3 (ENSG00000105997), HOXA5 (ENSG00000106004), HOXA6 (ENSG00000106006), HOXA13 (ENSG00000106031), TLX1 (ENSG00000107807), HOXB6 (ENSG00000108511), TLX2 (ENSG00000115297), HOXB8 (ENSG00000120068), HOXB5 (ENSG00000120075), HOXB3 (ENSG00000120093), HOXB1 (ENSG00000120094), HOXA7 (ENSG00000122592), HOXC13 (ENSG00000123364), HOXC11 (ENSG00000123388), HOXC12 (ENSG00000123407), HOXD1 (ENSG00000128645), HOXD3 (ENSG00000128652), HOXD9 (ENSG00000128709), HOXD10 (ENSG00000128710), HOXD11 (ENSG00000128713), HOXD13 (ENSG00000128714), PDX1 (ENSG00000139515), HOXB13 (ENSG00000159184), HOXD4 (ENSG00000170166), HOXD12 (ENSG00000170178), HOXB9 (ENSG00000170689), HOXC5 (ENSG00000172789), HOXB2 (ENSG00000173917), HOXD8 (ENSG00000175879), GSX2 (ENSG00000180613), HOXC9 (ENSG00000180806), HOXC10 (ENSG00000180818), HOXB4 (ENSG00000182742), HOXA4 (ENSG00000197576), HOXC6 (ENSG00000197757), HOXC4 (ENSG00000198353)

Protein

Protein identifiers

T-cell leukemia homeobox protein 3 — O43711 (reviewed: O43711)

Alternative names: Homeobox protein Hox-11L2

All UniProt accessions (1): O43711

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

RefSeq proteins (1): NP_066305* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001356	HD	Domain
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR017970	Homeobox_CS	Conserved_site
IPR020479	HD_metazoa	Domain
IPR042247	TLX1/2/3	Family

Pfam: PF00046

UniProt features (6 total): sequence conflict 3, chain 1, DNA-binding region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O43711-F1	68.52	0.28

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 112 (showing top): RNGTGGGC_UNKNOWN, CREL_01, GOBP_RESPIRATORY_GASEOUS_EXCHANGE_BY_RESPIRATORY_SYSTEM, GOBP_NEGATIVE_REGULATION_OF_NEURON_DIFFERENTIATION, BENPORATH_ES_WITH_H3K27ME3, TTCCGTT_MIR191, GOBP_REGULATION_OF_RESPIRATORY_SYSTEM_PROCESS, TATTATA_MIR374, GOBP_RESPIRATORY_SYSTEM_PROCESS, GOBP_NEUROGENESIS, FOXO4_01, CATRRAGC_UNKNOWN, SOX9_B1, GOBP_REGULATION_OF_NEURON_DIFFERENTIATION, NF1_Q6_01

GO Biological Process (11): neuron migration (GO:0001764), regulation of respiratory gaseous exchange by nervous system process (GO:0002087), regulation of transcription by RNA polymerase II (GO:0006357), central nervous system development (GO:0007417), respiratory gaseous exchange by respiratory system (GO:0007585), negative regulation of neuron differentiation (GO:0045665), animal organ development (GO:0048513), neuron fate specification (GO:0048665), GABAergic neuron differentiation (GO:0097154), regulation of DNA-templated transcription (GO:0006355), neuron differentiation (GO:0030182)

GO Molecular Function (5): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515)

GO Cellular Component (3): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
generation of neurons	2
regulation of DNA-templated transcription	2
neuron differentiation	2
cellular anatomical structure	2
cell migration	1
respiratory gaseous exchange by respiratory system	1
regulation of respiratory system process	1
nervous system process	1
transcription by RNA polymerase II	1
nervous system development	1
system development	1
multicellular organismal process	1
negative regulation of cell differentiation	1
regulation of neuron differentiation	1
anatomical structure development	1
cell fate specification	1
neuron fate commitment	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cell differentiation	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
binding	1
chromosome	1
intracellular membrane-bounded organelle	1
nuclear lumen	1

Protein interactions and networks

STRING

944 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TLX3	PHF6	Q8IWS0	896
TLX3	LYL1	P12980	851
TLX3	NUP214	P35658	848
TLX3	TAL1	P17542	824
TLX3	BCL11B	Q9C0K0	812
TLX3	LMO1	P25800	807
TLX3	RANBP17	Q9H2T7	797
TLX3	LMO2	P25791	750
TLX3	ABL1	P00519	738
TLX3	TAL2	Q16559	653
TLX3	LMX1B	O60663	650
TLX3	RUNX1	Q01196	637
TLX3	CDKN2A	P42771	597
TLX3	AGRN	O00468	586
TLX3	IKZF1	Q13422	585

IntAct

295 interactions, top by confidence:

A	B	Type	Score
TLX3	NHLRC4	psi-mi:“MI:0915”(physical association)	0.560
TLX3	IGFL2	psi-mi:“MI:0915”(physical association)	0.560
TLX3	PLAAT1	psi-mi:“MI:0915”(physical association)	0.560
TLX3	APBB1IP	psi-mi:“MI:0915”(physical association)	0.560
TLX3	KRT34	psi-mi:“MI:0915”(physical association)	0.560
TLX3	PRR20D	psi-mi:“MI:0915”(physical association)	0.560
CRX	TLX3	psi-mi:“MI:0915”(physical association)	0.560
TLX3	POU6F2	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	TLX3	psi-mi:“MI:0915”(physical association)	0.560
TLX3	MAGED1	psi-mi:“MI:0915”(physical association)	0.560
KRTAP6-3	TLX3	psi-mi:“MI:0915”(physical association)	0.560
TLX3	SMU1	psi-mi:“MI:0915”(physical association)	0.560
TLX3	REL	psi-mi:“MI:0915”(physical association)	0.560
TLX3	EFEMP2	psi-mi:“MI:0915”(physical association)	0.560
TLX3	FOSB	psi-mi:“MI:0915”(physical association)	0.560
TLX3	KCNJ5-AS1	psi-mi:“MI:0915”(physical association)	0.560
TLX3	INTS11	psi-mi:“MI:0915”(physical association)	0.560
TLX3	WDR83	psi-mi:“MI:0915”(physical association)	0.560
TLX3	GGTLC2	psi-mi:“MI:0915”(physical association)	0.560
TLX3	CEACAM6	psi-mi:“MI:0915”(physical association)	0.560
TLX3	HSPB2	psi-mi:“MI:0915”(physical association)	0.560
TLX3	UFSP1	psi-mi:“MI:0915”(physical association)	0.560
PLA2G10	TLX3	psi-mi:“MI:0915”(physical association)	0.560
TLX3	FNTB	psi-mi:“MI:0915”(physical association)	0.560
TLX3	MSX2	psi-mi:“MI:0915”(physical association)	0.560
ZNF44	TLX3	psi-mi:“MI:0915”(physical association)	0.560
TLX3	TCIRG1	psi-mi:“MI:0915”(physical association)	0.560
OIP5	TLX3	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (265): TLX3 (Affinity Capture-MS), TLX3 (Two-hybrid), TLX3 (Two-hybrid), TLX3 (Two-hybrid), TLX3 (Two-hybrid), TLX3 (Two-hybrid), TLX3 (Two-hybrid), TLX3 (Two-hybrid), TLX3 (Two-hybrid), TLX3 (Two-hybrid), TLX3 (Two-hybrid), TLX3 (Two-hybrid), TLX3 (Two-hybrid), TLX3 (Two-hybrid), TLX3 (Two-hybrid)

ESM2 similar proteins: A1YEY5, A1YFA5, A1YFI3, A1YG57, A2T733, A2T764, A2T7P4, A6NJ46, O42115, O43248, O43711, O55144, O95096, P02830, P09023, P09024, P09629, P09633, P17509, P17919, P18864, P23410, P28362, P29454, P31259, P31311, P31313, P31315, P42586, P43120, P43345, P43697, P48031, P52951, P53544, P53545, P53546, P56915, P97334, Q02591

Diamond homologs: A0JPN1, A1YG85, A5PKG8, A6NJ46, A6NMT0, A7MB54, A9L937, B0VXK3, D2KQB0, E7FDX5, M0R6D8, O08686, O13023, O35762, O42365, O43364, O43711, O55144, O88181, O93366, O93367, O93590, P0C1T1, P10035, P14652, P14837, P20009, P28468, P31245, P31246, P31261, P31314, P42583, P42584, P43120, P43345, P43688, P50219, P52945, P52950

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
TLX3	“down-regulates activity”	ETS1	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 83 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
Keratinization	10	12.7×	8e-07

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	38
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

443 predictions. Top by Δscore:

Variant	Effect	Δscore
5:171309782:CACAG:C	donor_loss	1.0000
5:171309785:AGG:A	donor_loss	1.0000
5:171309786:GGTG:G	donor_loss	1.0000
5:171309787:GTG:G	donor_loss	1.0000
5:171310394:G:GG	donor_gain	1.0000
5:171311381:C:A	acceptor_gain	1.0000
5:171309788:T:A	donor_loss	0.9900
5:171310148:A:AG	acceptor_gain	0.9900
5:171310148:AGC:A	acceptor_gain	0.9900
5:171310148:AGCG:A	acceptor_gain	0.9900
5:171310149:G:GG	acceptor_gain	0.9900
5:171310149:GC:G	acceptor_gain	0.9900
5:171310149:GCG:G	acceptor_gain	0.9900
5:171310149:GCGG:G	acceptor_gain	0.9900
5:171310149:GCGGC:G	acceptor_gain	0.9900
5:171310390:GGCG:G	donor_gain	0.9900
5:171310391:GCG:G	donor_gain	0.9900
5:171310391:GCGG:G	donor_gain	0.9900
5:171310392:CGGT:C	donor_loss	0.9900
5:171310394:G:T	donor_loss	0.9900
5:171310395:T:G	donor_loss	0.9900
5:171311384:TGCA:T	acceptor_loss	0.9900
5:171311385:GCA:G	acceptor_loss	0.9900
5:171311386:CA:C	acceptor_loss	0.9900
5:171311387:A:AC	acceptor_loss	0.9900
5:171311387:A:AG	acceptor_gain	0.9900
5:171311388:G:GG	acceptor_gain	0.9900
5:171311388:GGC:G	acceptor_gain	0.9900
5:171310145:CGCA:C	acceptor_loss	0.9800
5:171310146:GCAGC:G	acceptor_loss	0.9800

AlphaMissense

1883 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:171309417:T:C	F18L	1.000
5:171309419:C:A	F18L	1.000
5:171309419:C:G	F18L	1.000
5:171309433:T:C	I23T	1.000
5:171309744:T:A	W127R	1.000
5:171309744:T:C	W127R	1.000
5:171310191:G:C	G155R	1.000
5:171310192:G:A	G155D	1.000
5:171310194:C:G	H156D	1.000
5:171310195:A:G	H156R	1.000
5:171310196:C:A	H156Q	1.000
5:171310196:C:G	H156Q	1.000
5:171310200:T:G	Y158D	1.000
5:171310229:G:C	K167N	1.000
5:171310229:G:T	K167N	1.000
5:171310230:A:G	K168E	1.000
5:171310236:C:A	R170S	1.000
5:171310236:C:T	R170C	1.000
5:171310237:G:A	R170H	1.000
5:171310245:T:A	F173I	1.000
5:171310245:T:C	F173L	1.000
5:171310245:T:G	F173V	1.000
5:171310246:T:C	F173S	1.000
5:171310246:T:G	F173C	1.000
5:171310247:T:A	F173L	1.000
5:171310247:T:G	F173L	1.000
5:171310249:C:T	S174F	1.000
5:171310259:G:C	Q177H	1.000
5:171310259:G:T	Q177H	1.000
5:171310261:T:A	I178N	1.000

dbSNP variants (sampled 300 via entrez): RS1000015048 (5:171307254 G>A), RS1000129038 (5:171310250 C>A,T), RS1001521091 (5:171311314 A>G), RS1001792934 (5:171308172 G>A), RS1002140507 (5:171307900 C>A), RS1002205158 (5:171307665 A>T), RS1002522856 (5:171308718 C>T), RS1002706405 (5:171307939 A>C), RS1002950651 (5:171308997 G>A), RS1004039289 (5:171309362 C>A,T), RS1004132766 (5:171309528 A>G,T), RS1004651656 (5:171309844 G>A,C), RS1005318457 (5:171312294 G>A), RS1005721989 (5:171310753 C>T), RS1005815294 (5:171310919 G>A,C,T)

Disease associations

OMIM: gene MIM:604640 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): hereditary breast ovarian cancer syndrome (MONDO:0003582)

Orphanet (1): Hereditary breast and/or ovarian cancer syndrome (Orphanet:145)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST010989_258	Body size at age 10	2.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009819	comparative body size at age 10, self-reported

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D061325	Hereditary Breast and Ovarian Cancer Syndrome	C04.588.180.483; C04.588.322.455.431; C04.700.517; C12.050.351.500.056.630.705.431; C12.050.351.937.418.685.431; C12.100.250.056.630.705.431; C12.900.418.685.431; C16.320.700.517; C17.800.090.500.483; C19.344.410.431; C19.391.630.705.431

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
arsenite	increases methylation	1
potassium chromate(VI)	increases expression	1
clothianidin	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Doxorubicin	increases expression	1
Lead	affects expression	1
S-Nitrosoglutathione	increases expression	1

Cellosaurus cell lines

4 cell lines: 3 embryonic stem cell, 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_2022	DND-41	Cancer cell line	Male
CVCL_A7N2	SEES3-1V human TLX3, clone1	Embryonic stem cell	Male
CVCL_A7N3	SEES3-1V human TLX3, clone2	Embryonic stem cell	Male
CVCL_A7N4	SEES3-1V human TLX3, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT02562170	PHASE4	COMPLETED	Protexa® Versus TiLoopBra® in Immediate Breast Reconstruction- A Pilot Study
NCT00673335	PHASE3	COMPLETED	Letrozole in Preventing Breast Cancer in Postmenopausal Women With a BRCA1 or BRCA2 Mutation
NCT00685256	PHASE3	COMPLETED	Standard Genetic Counseling With or Without a Decision Guide in Improving Communication Between Mothers Undergoing BRCA1/2 Testing and Their Minor-Age Children
NCT03162276	PHASE3	UNKNOWN	Trial of Inquiry Based Stress Reduction (IBSR) Program for BRCA1/2 Mutation Carriers
NCT00253539	PHASE2	COMPLETED	Arzoxifene or Tamoxifen in Preventing Breast Cancer in Premenopausal Women at High Risk for Breast Cancer
NCT00305695	PHASE2	COMPLETED	Zoledronate or Observation in Maintaining Bone Mineral Density in Patients Who Are Undergoing Surgery to Remove Both Ovaries
NCT00321633	PHASE2	COMPLETED	Carboplatin or Docetaxel in Treating Women With Metastatic Genetic Breast Cancer
NCT01333748	PHASE2	COMPLETED	Search Allelic Imbalance of Expression of BRCA Genes in Hereditary Risk of Breast and/or Ovarian Cancer
NCT01367639	PHASE2	COMPLETED	Trial of Inquiry Based Stress Reduction (IBSR) Program for BRCA1/2 Mutation Carriers
NCT00535119	PHASE1	COMPLETED	Veliparib, Carboplatin, and Paclitaxel in Treating Patients With Advanced Solid Cancer
NCT00892736	PHASE1	COMPLETED	Veliparib in Treating Patients With Malignant Solid Tumors That Do Not Respond to Previous Therapy
NCT03832985	EARLY_PHASE1	COMPLETED	Pediatric Reporting of Adult-Onset Genomic Results
NCT00005095	Not specified	RECRUITING	Specimen and Data Study for Ovarian Cancer Early Detection and Prevention
NCT00609505	Not specified	COMPLETED	Telemedicine vs. Face-to-Face Cancer Genetic Counseling
NCT01273909	Not specified	UNKNOWN	Outcomes After Perforator Flap Reconstruction for Breast Reconstruction and/or Lymphedema Treatment
NCT01445275	Not specified	WITHDRAWN	Cost of Cancer Risk Management in Women at Elevated Genetic Risk for Ovarian Cancer Who Participated on GOG-0199
NCT01608074	Not specified	ACTIVE_NOT_RECRUITING	Radical Fimbriectomy for Young BRCA Mutation Carriers
NCT02087592	Not specified	COMPLETED	Feasibility of Lifestyle Intervention in BRCA1/2 Mutation Carriers
NCT02302742	Not specified	RECRUITING	Triple Negative Breast Cancer and Germline Hereditary Breast and Ovarian Cancer Mutation Carrier Registry
NCT02324062	Not specified	COMPLETED	Cancer Genetics Hereditary Cancer Panel Testing
NCT02516540	Not specified	UNKNOWN	Efficacy of Lifestyle Intervention in BRCA1/2 Mutation Carriers
NCT02653105	Not specified	ACTIVE_NOT_RECRUITING	Women at Risk of Breast Cancer and OLFM4
NCT02705924	Not specified	TERMINATED	Impact of a Psychoeducational Intervention on Expectations and Coping in Young Women Exposed to a High HBOC Risk
NCT02760849	Not specified	ACTIVE_NOT_RECRUITING	Surgery in Preventing Ovarian Cancer in Patients With Genetic Mutations
NCT02786147	Not specified	COMPLETED	Identification and Referral of Women at Risk for Hereditary Breast/Ovarian Cancer
NCT02956681	Not specified	COMPLETED	Statewide Communication to Reach Diverse Low Income Women
NCT03015376	Not specified	UNKNOWN	Inherited Susceptible Genes Among Epithelial Ovarian Cancer
NCT03050268	Not specified	RECRUITING	Familial Investigations of Childhood Cancer Predisposition
NCT03075540	Not specified	COMPLETED	Enhancing At-risk Latina Women’s Use of Genetic Counseling for Hereditary Breast and Ovarian Cancer
NCT03124212	Not specified	RECRUITING	Cascade Genetic Testing for Hereditary Breast/Ovarian Cancer and Lynch Syndrome in Switzerland
NCT03246841	Not specified	ACTIVE_NOT_RECRUITING	Investigation of Tumour Spectrum of Germline Mutations in Breast and Ovarian Cancer Genes.
NCT03294343	Not specified	UNKNOWN	Risk-Reducing Surgeries for Hereditary Ovarian Cancer
NCT03421327	Not specified	COMPLETED	Genetic Risk: Whether, When, and How to Tell Adolescents
NCT03510689	Not specified	COMPLETED	Genetics and Heart Health After Cancer Therapy
NCT03511690	Not specified	COMPLETED	Testing an Intelligent Tutoring System to Enhance Genetic Risk Assessment
NCT03784859	Not specified	COMPLETED	Tissue Expansion in Breast Reconstruction Without Drains
NCT03979612	Not specified	UNKNOWN	Evaluation of the Adhesion to the GENEPY Network
NCT04197856	Not specified	ACTIVE_NOT_RECRUITING	Direct Information to At-risk Relatives
NCT04407611	Not specified	COMPLETED	Scalable Communication Modalities for Returning Genetic Research Results
NCT04508764	Not specified	TERMINATED	Implementation of the Families Accelerating Cascade Testing Toolkit (FACTT) for Hereditary Breast and Ovarian Cancer and Lynch Syndrome