UPF3A

Summary

UPF3A (UPF3A regulator of nonsense mediated mRNA decay, HGNC:20332) is a protein-coding gene on chromosome 13q34, encoding Regulator of nonsense transcripts 3A (Q9H1J1). Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery.

This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. The encoded protein is one of two functional homologs to yeast Upf3p. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. It forms with Y14 a complex that binds specifically 20 nt upstream of exon-exon junctions. This gene is located on the long arm of chromosome 13. Several splice variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 65110 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 113 total
• MANE Select transcript: NM_023011

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20332
Approved symbol	UPF3A
Name	UPF3A regulator of nonsense mediated mRNA decay
Location	13q34
Locus type	gene with protein product
Status	Approved
Aliases	RENT3A, UPF3, HUPF3A
Ensembl gene	ENSG00000169062
Ensembl biotype	protein_coding
OMIM	605530
Entrez	65110

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 12 protein_coding, 7 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000351487, ENST00000375299, ENST00000474056, ENST00000475218, ENST00000479712, ENST00000480362, ENST00000481131, ENST00000484246, ENST00000492270, ENST00000493727, ENST00000618700, ENST00000619079, ENST00000880098, ENST00000880099, ENST00000915711, ENST00000915712, ENST00000915713, ENST00000915714, ENST00000915715, ENST00000966312, ENST00000966313

RefSeq mRNA: 9 — MANE Select: NM_023011 NM_001353644, NM_001353645, NM_001353646, NM_001353647, NM_001353648, NM_001353649, NM_001353650, NM_023011, NM_080687

CCDS: CCDS9543, CCDS9544

Canonical transcript exons

ENST00000375299 — 10 exons

Exon	Start	End
ENSE00001888625	114281601	114281846
ENSE00003541834	114298840	114299000
ENSE00003579217	114282021	114282127
ENSE00003585272	114301731	114302025
ENSE00003619119	114291489	114291544
ENSE00003631011	114282837	114282943
ENSE00003662765	114286302	114286400
ENSE00003678052	114291634	114291792
ENSE00003681086	114286519	114286629
ENSE00003715351	114304789	114305817

Expression profiles

Bgee: expression breadth ubiquitous, 191 present calls, max score 98.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.1642 / max 245.5548, expressed in 1787 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
136290	8.1421	1747
136295	1.2929	860
136291	1.1591	741
136294	0.3230	138
136293	0.1737	54
136292	0.0734	16

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	98.74	gold quality
cerebellar hemisphere	UBERON:0002245	98.60	gold quality
sural nerve	UBERON:0015488	98.48	gold quality
cerebellar cortex	UBERON:0002129	98.47	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	97.83	gold quality
right uterine tube	UBERON:0001302	97.81	gold quality
right lobe of thyroid gland	UBERON:0001119	97.58	gold quality
left lobe of thyroid gland	UBERON:0001120	97.58	gold quality
left testis	UBERON:0004533	97.41	gold quality
right testis	UBERON:0004534	97.18	gold quality
body of pancreas	UBERON:0001150	96.81	gold quality
cortical plate	UBERON:0005343	96.78	gold quality
ganglionic eminence	UBERON:0004023	96.74	gold quality
right frontal lobe	UBERON:0002810	96.62	gold quality
adenohypophysis	UBERON:0002196	96.53	gold quality
metanephros cortex	UBERON:0010533	96.48	gold quality
ventricular zone	UBERON:0003053	96.43	gold quality
mucosa of stomach	UBERON:0001199	96.36	gold quality
body of uterus	UBERON:0009853	96.26	gold quality
tibial nerve	UBERON:0001323	96.25	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	96.13	gold quality
right ovary	UBERON:0002118	96.06	gold quality
endocervix	UBERON:0000458	96.05	gold quality
thyroid gland	UBERON:0002046	96.02	gold quality
left uterine tube	UBERON:0001303	95.94	gold quality
calcaneal tendon	UBERON:0003701	95.87	gold quality
left ovary	UBERON:0002119	95.77	gold quality
muscle layer of sigmoid colon	UBERON:0035805	95.76	gold quality
anterior cingulate cortex	UBERON:0009835	95.75	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	95.59	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.98
E-MTAB-6524	no	214.13
E-HCAD-31	no	2.17

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 11)

• binds to spliced mRNAs upstream of exon-exon junctions; is part of mRNP complexes that are ready for nuclear export and that participate in nonsense-mediated mRNA decay (PMID:11546873)
• The complex between the interacting domains of human UPF2 and UPF3b at a 1.95 A resolution. (PMID:15004547)
• hUpf3a is much less active than hUpf3b to induce NMD and to stimulate translation (PMID:16601204)
• The Upf complex communicates with the exon-junction complex and triggers nonsense-mediated decay in the cytoplasm. (PMID:17803942)
• Results suggest that UPF3A levels are tightly regulated by a post-transcriptional switch to maintain appropriate levels of NMD substrates in cells containing different levels of UPF3B. (PMID:19503078)
• Study observed that CHERP and its binding partner SR140 are significantly upregulated in human clinical colorectal cancer tissues (CRC) and clarified how CHERP/SR140 exert an oncogenic role in CRC development partially through regulating expression of UPF3A variants. (PMID:30977118)
• (Phospho)proteomic Profiling of Microsatellite Unstable CRC Cells Reveals Alterations in Nuclear Signaling and Cholesterol Metabolism Caused by Frameshift Mutation of NMD Regulator UPF3A. (PMID:32718059)
• Human UPF3A and UPF3B enable fault-tolerant activation of nonsense-mediated mRNA decay. (PMID:35451084)
• Mammalian UPF3A and UPF3B can activate nonsense-mediated mRNA decay independently of their exon junction complex binding. (PMID:35451102)
• Structures of nonsense-mediated mRNA decay factors UPF3B and UPF3A in complex with UPF2 reveal molecular basis for competitive binding and for neurodevelopmental disorder-causing mutation. (PMID:35640974)
• Genetic compensation response could exist in colorectal cancer: UPF3A upregulates the oncogenic homologue gene SRSF3 expression corresponding to SRSF6 to promote colorectal cancer metastasis. (PMID:36807382)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	upf3a	ENSDARG00000069297
mus_musculus	Upf3a	ENSMUSG00000038398
rattus_norvegicus	Upf3a	ENSRNOG00000017397
drosophila_melanogaster	Upf3	FBGN0034923
caenorhabditis_elegans		WBGENE00004882

Paralogs (1): UPF3B (ENSG00000125351)

Protein

Protein identifiers

Regulator of nonsense transcripts 3A — Q9H1J1 (reviewed: Q9H1J1)

Alternative names: Nonsense mRNA reducing factor 3A, Up-frameshift suppressor 3 homolog A

All UniProt accessions (2): Q9H1J1, A0A087WZ33

UniProt curated annotations — full annotation on UniProt →

Function. Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery. Recruits UPF2 at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. However, UPF3A is shown to be only marginally active in NMD as compared to UPF3B. Binds spliced mRNA upstream of exon-exon junctions. In vitro, weakly stimulates translation.

Subunit / interactions. Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Associates with the exon junction complex (EJC). Interacts with UPF2 and RBM8A. Interacts with DHX34; the interaction is RNA-independent.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Isoform 1 is strongly expressed in testis, uterus, muscle, fetal brain and spinal cord. Isoform 2 is strongly expressed in fetal brain and spinal cord.

Similarity. Belongs to the RENT3 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9H1J1-1	1, hUpf3p, hUPF3L	yes
Q9H1J1-2	2, hUpf3pdelta, hUPF3S
Q9H1J1-3	3

RefSeq proteins (9): NP_001340573, NP_001340574, NP_001340575, NP_001340576, NP_001340577, NP_001340578, NP_001340579, NP_075387, NP_542418 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005120	UPF3_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR039722	Upf3	Family

Pfam: PF03467

UniProt features (27 total): strand 7, region of interest 4, helix 4, compositionally biased region 4, splice variant 2, chain 1, sequence variant 1, mutagenesis site 1, sequence conflict 1, turn 1, modified residue 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7QG6	X-RAY DIFFRACTION	2.95
2L08	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H1J1-F1	63.19	0.14

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 (1): 341

Mutagenesis-validated functional residues (1):

Position	Phenotype
432	increases nmd activity and translation stimulation.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-9010553	Regulation of expression of SLITs and ROBOs
R-HSA-975957	Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)

MSigDB gene sets: 171 (showing top): MORF_DNMT1, MODULE_451, GCM_GSPT1, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_RNA_SPLICING, GOBP_POSITIVE_REGULATION_OF_MRNA_PROCESSING, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_REGULATION_OF_CATABOLIC_PROCESS, BLALOCK_ALZHEIMERS_DISEASE_UP, chr13q34, GOBP_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT, GOBP_RNA_SPLICING, MORF_PRKDC

GO Biological Process (8): in utero embryonic development (GO:0001701), spermatogenesis (GO:0007283), positive regulation of translation (GO:0045727), mRNA transport (GO:0051028), random inactivation of X chromosome (GO:0060816), positive regulation of mRNA cis splicing, via spliceosome (GO:1905746), negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623), nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)

GO Molecular Function (6): mRNA binding (GO:0003729), telomeric repeat DNA binding (GO:0042162), protein sequestering activity (GO:0140311), nucleic acid binding (GO:0003676), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (8): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886), exon-exon junction complex (GO:0035145), neuron projection (GO:0043005)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Signaling by ROBO receptors	1
Nonsense-Mediated Decay (NMD)	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
binding	2
nuclear lumen	2
chordate embryonic development	1
developmental process involved in reproduction	1
male gamete generation	1
translation	1
regulation of translation	1
positive regulation of gene expression	1
positive regulation of protein metabolic process	1
RNA transport	1
dosage compensation by inactivation of X chromosome	1
mRNA cis splicing, via spliceosome	1
positive regulation of mRNA splicing, via spliceosome	1
regulation of mRNA cis splicing, via spliceosome	1
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	1
negative regulation of mRNA catabolic process	1
regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	1
nuclear-transcribed mRNA catabolic process	1
RNA binding	1
sequence-specific DNA binding	1
protein binding	1
molecular sequestering activity	1
nucleic acid binding	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1
intracellular anatomical structure	1
cytoplasm	1
membrane	1
cell periphery	1
nuclear protein-containing complex	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

906 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UPF3A	UPF2	Q9HAU5	999
UPF3A	UPF1	Q92900	999
UPF3A	SMG1	Q96Q15	998
UPF3A	MAGOHB	Q96A72	969
UPF3A	MAGOH	P50606	969
UPF3A	SMG5	Q9UPR3	960
UPF3A	EIF4A3	P38919	951
UPF3A	SMG9	Q9H0W8	947
UPF3A	SMG8	Q8ND04	945
UPF3A	SMG7	Q92540	930
UPF3A	SMG6	Q86US8	929
UPF3A	RBM8A	Q9Y5S9	924
UPF3A	NCBP1	Q09161	910
UPF3A	RNPS1	Q15287	886
UPF3A	NCBP2	P52298	857

IntAct

35 interactions, top by confidence:

A	B	Type	Score
UPF2	UPF1	psi-mi:“MI:0914”(association)	0.960
UPF1	UPF3B	psi-mi:“MI:0914”(association)	0.890
HNRNPC	HNRNPA1	psi-mi:“MI:0914”(association)	0.790
UPF2	UPF3A	psi-mi:“MI:0407”(direct interaction)	0.770
UPF3A	UPF2	psi-mi:“MI:0915”(physical association)	0.770
SMG1	UPF1	psi-mi:“MI:0914”(association)	0.760
RBM8A	UPF1	psi-mi:“MI:0914”(association)	0.730
RBM8A	UPF3A	psi-mi:“MI:0915”(physical association)	0.660
SMG1	MAGOH	psi-mi:“MI:0914”(association)	0.640
UPF3A	UPF1	psi-mi:“MI:0915”(physical association)	0.560
ALYREF	UPF1	psi-mi:“MI:0914”(association)	0.530
UPF3A	UPF3B	psi-mi:“MI:0914”(association)	0.520
UPF3B	UPF3A	psi-mi:“MI:0407”(direct interaction)	0.520
UPF1	UPF1	psi-mi:“MI:0914”(association)	0.350
CEP43	CCHCR1	psi-mi:“MI:0914”(association)	0.350
WAPL	RPL10	psi-mi:“MI:0914”(association)	0.350
RNF41	CLEC16A	psi-mi:“MI:0914”(association)	0.350
Cbx1		psi-mi:“MI:0914”(association)	0.350
PHF8	MACROH2A1	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
RBM8A	HNRNPC	psi-mi:“MI:0914”(association)	0.350
UPF3A	HNRNPA1	psi-mi:“MI:0914”(association)	0.350
RNPS1	UPF1	psi-mi:“MI:0914”(association)	0.350
SRRM1	UPF1	psi-mi:“MI:0914”(association)	0.350
NXF1	UPF1	psi-mi:“MI:0914”(association)	0.350
SSRP1	DDX39A	psi-mi:“MI:0914”(association)	0.350
UPF3A	CASC3	psi-mi:“MI:0914”(association)	0.350
SLC27A6	NBAS	psi-mi:“MI:0914”(association)	0.350

BioGRID (71): UPF3A (Dosage Rescue), UPF3A (Reconstituted Complex), UPF3A (Affinity Capture-MS), UPF3A (Affinity Capture-MS), UPF3A (Affinity Capture-MS), UPF3A (Affinity Capture-MS), UPF3A (Affinity Capture-MS), UPF3A (Affinity Capture-MS), HBB (Affinity Capture-MS), CA1 (Affinity Capture-MS), HBA2 (Affinity Capture-MS), HBD (Affinity Capture-MS), CASC3 (Affinity Capture-MS), AGGF1 (Affinity Capture-MS), APOA1 (Affinity Capture-MS)

ESM2 similar proteins: A4D2P6, A6NNA2, A7MD48, A8IHN8, C9JLR9, G3V9M2, O00287, O95644, P04198, P12755, P18444, P49796, P49797, P51608, P55199, Q00566, Q08DA0, Q0PHV7, Q13387, Q1W6H9, Q29RS4, Q3UPL5, Q3YEC7, Q4QQU1, Q4VA45, Q5XKK7, Q61976, Q6NV74, Q6R891, Q7Z6J2, Q80WV7, Q80YR4, Q86UK7, Q8BKA3, Q8N554, Q8R149, Q8R4T5, Q8TF61, Q8VCG9, Q95LG8

Diamond homologs: B0S733, F1QNX7, Q10267, Q9BZI7, Q9FVW4, Q9H1J1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 32 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
mRNA 3’-end processing	8	60.6×	3e-11
Transport of Mature mRNA derived from an Intron-Containing Transcript	9	52.7×	6e-12
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)	9	33.8×	1e-10
mRNA Splicing	5	21.1×	6e-05
Processing of Capped Intron-Containing Pre-mRNA	6	19.0×	1e-05
mRNA Splicing - Major Pathway	9	18.9×	2e-08
Regulation of expression of SLITs and ROBOs	7	18.6×	2e-06
Metabolism of RNA	6	9.6×	4e-04

GO biological processes:

GO term	Partners	Fold	FDR
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	8	129.1×	9e-14
mRNA export from nucleus	9	91.8×	6e-14
mRNA splicing, via spliceosome	8	25.3×	5e-08
RNA splicing	6	18.2×	3e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	97
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1796 predictions. Top by Δscore:

Variant	Effect	Δscore
13:114281760:G:GT	donor_gain	1.0000
13:114281831:G:GT	donor_gain	1.0000
13:114282125:GAGGT:G	donor_loss	1.0000
13:114282127:GGTGA:G	donor_loss	1.0000
13:114282128:G:C	donor_loss	1.0000
13:114282129:T:G	donor_loss	1.0000
13:114291781:G:GG	donor_gain	1.0000
13:114301914:G:T	donor_gain	1.0000
13:114281763:GC:G	donor_gain	0.9900
13:114281843:CAAG:C	donor_loss	0.9900
13:114281844:AAGG:A	donor_loss	0.9900
13:114281845:AGG:A	donor_loss	0.9900
13:114281846:GGTGG:G	donor_loss	0.9900
13:114281847:GTGG:G	donor_loss	0.9900
13:114281848:T:A	donor_loss	0.9900
13:114282835:A:AG	acceptor_gain	0.9900
13:114282836:G:GG	acceptor_gain	0.9900
13:114286517:A:AG	acceptor_gain	0.9900
13:114286518:G:GG	acceptor_gain	0.9900
13:114291633:GA:G	acceptor_gain	0.9900
13:114291633:GAGA:G	acceptor_gain	0.9900
13:114291778:GAA:G	donor_gain	0.9900
13:114291786:GAT:G	donor_gain	0.9900
13:114301865:GGA:G	donor_gain	0.9900
13:114301866:GAG:G	donor_gain	0.9900
13:114301868:G:GG	donor_gain	0.9900
13:114301873:GA:G	donor_gain	0.9900
13:114301914:G:GT	donor_gain	0.9900
13:114304787:AGG:A	acceptor_loss	0.9900
13:114291632:A:AG	acceptor_gain	0.9800

AlphaMissense

3104 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:114282869:T:A	I116N	0.999
13:114282875:T:C	F118S	0.999
13:114282902:T:C	F127S	0.999
13:114286332:C:A	A151D	0.999
13:114281846:G:C	K69N	0.998
13:114281846:G:T	K69N	0.998
13:114282025:T:A	V71D	0.998
13:114282028:T:A	I72N	0.998
13:114282030:C:A	R73S	0.998
13:114282037:T:C	L75P	0.998
13:114282913:T:C	F131L	0.998
13:114282915:T:A	F131L	0.998
13:114282915:T:G	F131L	0.998
13:114282929:T:C	F136S	0.998
13:114286317:C:A	A146E	0.998
13:114286527:T:G	Y177D	0.998
13:114286536:T:C	F180L	0.998
13:114286537:T:C	F180S	0.998
13:114286538:T:A	F180L	0.998
13:114286538:T:G	F180L	0.998
13:114291507:T:A	L217H	0.998
13:114291662:G:C	R239P	0.998
13:114282037:T:A	L75Q	0.997
13:114282064:T:C	L84P	0.997
13:114282863:C:A	A114E	0.997
13:114282869:T:G	I116S	0.997
13:114286528:A:C	Y177S	0.997
13:114291507:T:C	L217P	0.997
13:114282869:T:C	I116T	0.996
13:114282901:T:C	F127L	0.996

dbSNP variants (sampled 300 via entrez): RS1000041544 (13:114289705 T>G), RS1000120348 (13:114291350 C>T), RS1000186409 (13:114292519 C>T), RS1000249106 (13:114284972 C>G), RS1000606194 (13:114305116 A>G), RS1000817866 (13:114299556 C>T), RS1000834454 (13:114280896 A>G), RS1000846780 (13:114286982 AG>A), RS1000899322 (13:114287208 A>G), RS1001046892 (13:114281967 T>A,C,G), RS1001096954 (13:114288684 G>A), RS1001203967 (13:114306288 TAAA>T,TA,TAA,TAAAA,TAAAAA), RS1001222804 (13:114283769 C>G,T), RS1001253679 (13:114283934 A>T), RS1001415793 (13:114281795 C>T)

Disease associations

OMIM: gene MIM:605530 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST005211_6	Nodular sclerosis Hodgkin lymphoma	5.000000e-08
GCST007269_324	Pulse pressure	1.000000e-09
GCST008839_439	Height	1.000000e-11
GCST90020028_1229	Hip circumference adjusted for BMI	3.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005763	pulse pressure measurement
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, decreases methylation	5
aristolochic acid I	decreases expression	1
bisphenol F	affects cotreatment, decreases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects methylation	1
beta-lapachone	increases expression, decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	affects cotreatment, decreases expression	1
Temozolomide	decreases expression	1
Sunitinib	increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression, increases abundance	1
Caffeine	increases phosphorylation	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Hydrogen Peroxide	affects expression	1
Indomethacin	affects cotreatment, decreases expression	1
Lead	affects splicing	1
Methyl Methanesulfonate	increases expression	1
Selenium	decreases expression, affects cotreatment	1
Vitamin E	affects cotreatment, decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases expression, increases abundance	1
tert-Butylhydroperoxide	decreases expression	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_E2ND	HAP1 UPF3A (-) 1	Cancer cell line	Male
CVCL_E2NE	HAP1 UPF3A (-) 2	Cancer cell line	Male
CVCL_E2NF	HAP1 UPF3A (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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