ARFRP1

Summary

ARFRP1 (ARF related protein 1, HGNC:662) is a protein-coding gene on chromosome 20q13.33, encoding ADP-ribosylation factor-related protein 1 (Q13795). Trans-Golgi-associated GTPase that regulates protein sorting. It is a selective cancer dependency (DepMap: 76.0% of cell lines).

The protein encoded by this gene is a membrane-associated GTP-ase which localizes to the plasma membrane and is related to the ADP-ribosylation factor (ARF) and ARF-like (ARL) proteins. This gene plays a role in membrane trafficking between the trans-Golgi network and endosomes. Alternatively spliced transcript variants encoding different isoforms have been identified.

Source: NCBI Gene 10139 — RefSeq curated summary.

At a glance

• GWAS associations: 13
• Clinical variants (ClinVar): 51 total — 1 pathogenic
• Cancer dependency (DepMap): dependent in 76.0% of screened cell lines
• MANE Select transcript: NM_001267547

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:662
Approved symbol	ARFRP1
Name	ARF related protein 1
Location	20q13.33
Locus type	gene with protein product
Status	Approved
Aliases	ARP, Arp1, ARL18
Ensembl gene	ENSG00000101246
Ensembl biotype	protein_coding
OMIM	604699
Entrez	10139

Gene structure

Transcript identifiers

Ensembl transcripts: 31 — 24 protein_coding, 4 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000424545, ENST00000607873, ENST00000609188, ENST00000609537, ENST00000610414, ENST00000610774, ENST00000612157, ENST00000612256, ENST00000612772, ENST00000614942, ENST00000618568, ENST00000618838, ENST00000619493, ENST00000622789, ENST00000878281, ENST00000878282, ENST00000878283, ENST00000878284, ENST00000878285, ENST00000878286, ENST00000878287, ENST00000915675, ENST00000915676, ENST00000915677, ENST00000964412, ENST00000964413, ENST00000964414, ENST00000964415, ENST00000964416, ENST00000964417, ENST00000964418

RefSeq mRNA: 8 — MANE Select: NM_001267547 NM_001134758, NM_001267544, NM_001267545, NM_001267546, NM_001267547, NM_001267548, NM_001267549, NM_003224

CCDS: CCDS13533, CCDS46630, CCDS68172, CCDS68173

Canonical transcript exons

ENST00000622789 — 8 exons

Exon	Start	End
ENSE00000856625	63700602	63700702
ENSE00001172753	63702136	63702217
ENSE00003641165	63706357	63706439
ENSE00003725649	63706651	63706738
ENSE00003844002	63698647	63700530
ENSE00003845160	63707867	63707976
ENSE00003892303	63706999	63707097
ENSE00003893670	63701830	63701900

Expression profiles

Bgee: expression breadth ubiquitous, 289 present calls, max score 96.15.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.9374 / max 64.1693, expressed in 1802 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
188406	9.2002	1790
188407	2.7372	1378

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
type B pancreatic cell	CL:0000169	96.15	gold quality
apex of heart	UBERON:0002098	95.58	gold quality
olfactory bulb	UBERON:0002264	94.98	silver quality
mucosa of transverse colon	UBERON:0004991	94.89	gold quality
spleen	UBERON:0002106	93.08	gold quality
right frontal lobe	UBERON:0002810	93.06	gold quality
metanephros cortex	UBERON:0010533	92.67	gold quality
lower esophagus mucosa	UBERON:0035834	92.67	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.61	gold quality
stromal cell of endometrium	CL:0002255	92.43	gold quality
granulocyte	CL:0000094	92.36	gold quality
transverse colon	UBERON:0001157	92.34	gold quality
right atrium auricular region	UBERON:0006631	92.34	gold quality
adenohypophysis	UBERON:0002196	92.22	gold quality
heart left ventricle	UBERON:0002084	92.15	gold quality
tibial nerve	UBERON:0001323	92.13	gold quality
nucleus accumbens	UBERON:0001882	92.13	gold quality
putamen	UBERON:0001874	92.08	gold quality
cerebellar hemisphere	UBERON:0002245	92.08	gold quality
body of uterus	UBERON:0009853	92.07	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	92.07	gold quality
sural nerve	UBERON:0015488	92.03	gold quality
lower esophagus muscularis layer	UBERON:0035833	92.00	gold quality
cerebellar cortex	UBERON:0002129	91.97	gold quality
lower esophagus	UBERON:0013473	91.97	gold quality
endocervix	UBERON:0000458	91.96	gold quality
cingulate cortex	UBERON:0003027	91.93	gold quality
cardiac ventricle	UBERON:0002082	91.85	gold quality
anterior cingulate cortex	UBERON:0009835	91.79	gold quality
right uterine tube	UBERON:0001302	91.76	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.37
E-MTAB-4850	no	581.02
E-GEOD-124858	no	37.93

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

52 targeting ARFRP1, 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-340-5P	100.00	72.50	4437
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-1273H-5P	99.77	66.32	2471
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
HSA-MIR-4429	99.77	69.62	2111
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-21-5P	99.46	70.54	1035

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 76.0% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 13)

• Data show that ADP-ribosylation factor-related protein 1 (ARFRP1) is associated mainly with the trans-Golgi compartment and the trans-Golgi network (TGN) and is an essential regulatory factor for targeting of golgin-97 and golgin-245 onto Golgi membranes. (PMID:16129887)
• These data suggest that lethality of Arfrp1 knockout embryos is due to a specific disruption of protein targeting, e.g., of ARL1 and Golgin-245, to the Golgi. (PMID:17127620)
• Results show that ARL1 and ARFRP1 regulate retrograde transport of Shiga toxin to the TGN and anterograde transport of VSVG from the TGN, respectively. (PMID:19224922)
• The GTPase ARFRP1 controls the lipidation of chylomicrons in the Golgi of the intestinal epithelium. (PMID:22505585)
• Propose that Arfrp1 exposes a binding site on AP-1 that recognizes the Vangl2 sorting motif for capture into a transport vesicle destined for the proximal surface of a polarized epithelial cell. (PMID:23326640)
• One or more of 7 genes residing in a chromosome 20q13.3 CNV region appears to influence BMI. The strongest candidate is ARFRP1. (PMID:26881067)
• Results provide evidence that ARFRP1 is required for HCV propagation through its interaction with NS5A protein. Also, ARFRP1 is involved in the regulation of lipid droplet (LD) growth in HCV-infected cells and, recruits SNAP23 to sites in close proximity to LDs. (PMID:27550144)
• ARFRP1 shifted from a predominantly cis-Golgi and endosome-to-trans-Golgi network localization to localizing both Golgi and non-Golgi vesicular structures in hNaa30-depleted cells. (PMID:28356483)
• lack of Arfrp1 increases the abundance of lipolysis-modulating enzymes TERA/VCP, FAF2 and Plin2 at LDs, which might decrease lipolysis and reduce availability of fatty acids for triglyceride synthesis and their release via chylomicrons. (PMID:30348522)
• The ARFRP1 is a master regulator of retrograde-carrier tethering to the trans-Golgi network (TGN). (PMID:31575603)
• LncRNA ARFRP1 knockdown inhibits LPS-induced the injury of chondrocytes by regulation of NF-kappaB pathway through modulating miR-15a-5p/TLR4 axis. (PMID:32931797)
• The amphipathic helices of Arfrp1 and Arl14 are sufficient to determine subcellular localizations. (PMID:32972971)
• The ARFRP1-dependent Golgi scaffolding protein GOPC is required for insulin secretion from pancreatic beta-cells. (PMID:33359402)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	arfrp1	ENSDARG00000057857
mus_musculus	Arfrp1	ENSMUSG00000038671
rattus_norvegicus	Arfrp1	ENSRNOG00000013992
drosophila_melanogaster	Arfrp1	FBGN0030088
caenorhabditis_elegans	Y54E10BR.2	WBGENE00021841

Paralogs (30): ARF5 (ENSG00000004059), SAR1A (ENSG00000079332), TRIM23 (ENSG00000113595), ARL6 (ENSG00000113966), ARL1 (ENSG00000120805), ARL4A (ENSG00000122644), ARL8B (ENSG00000134108), ARF3 (ENSG00000134287), ARL3 (ENSG00000138175), ARL5C (ENSG00000141748), ARF1 (ENSG00000143761), ARL8A (ENSG00000143862), ARL11 (ENSG00000152213), SAR1B (ENSG00000152700), ARL5A (ENSG00000162980), ARF6 (ENSG00000165527), ARL5B (ENSG00000165997), ARF4 (ENSG00000168374), ARL13B (ENSG00000169379), ARL13A (ENSG00000174225), ARL10 (ENSG00000175414), ARL4D (ENSG00000175906), ARL14 (ENSG00000179674), ARL15 (ENSG00000185305), ARL17A (ENSG00000185829), ARL4C (ENSG00000188042), ARL9 (ENSG00000196503), ARL2 (ENSG00000213465), ARL16 (ENSG00000214087), ARL17B (ENSG00000228696)

Protein

Protein identifiers

ADP-ribosylation factor-related protein 1 — Q13795 (reviewed: Q13795)

All UniProt accessions (2): Q13795, A0A384P5U7

UniProt curated annotations — full annotation on UniProt →

Function. Trans-Golgi-associated GTPase that regulates protein sorting. Controls the targeting of ARL1 and its effector to the trans-Golgi. Required for the lipidation of chylomicrons in the intestine and required for VLDL lipidation in the liver.

Subunit / interactions. Interacts with SYS1.

Subcellular location. Golgi apparatus. trans-Golgi network.

Tissue specificity. Found in most tissues.

Similarity. Belongs to the small GTPase superfamily. Arf family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q13795-1	1	yes
Q13795-2	2
Q13795-3	3
Q13795-4	4

RefSeq proteins (8): NP_001128230, NP_001254473, NP_001254474, NP_001254475, NP_001254476, NP_001254477, NP_001254478, NP_003215 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005225	Small_GTP-bd	Domain
IPR006689	Small_GTPase_ARF/SAR	Family
IPR024156	Small_GTPase_ARF	Family
IPR027417	P-loop_NTPase	Homologous_superfamily

Pfam: PF00025

UniProt features (10 total): splice variant 4, binding site 3, chain 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q13795-F1	90.86	0.75

Functional residue map

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

Ligand- & substrate-binding residues (3): 24–31; 75–79; 134–137

Post-translational modifications (1): 1

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-6811440	Retrograde transport at the Trans-Golgi-Network
R-HSA-199991	Membrane Trafficking
R-HSA-5653656	Vesicle-mediated transport
R-HSA-6811442	Intra-Golgi and retrograde Golgi-to-ER traffic

MSigDB gene sets: 158 (showing top): GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_GOLGI_TO_PLASMA_MEMBRANE_TRANSPORT, GOCC_TRANS_GOLGI_NETWORK, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE, GOBP_GASTRULATION, GOBP_GOLGI_TO_PLASMA_MEMBRANE_PROTEIN_TRANSPORT, GOBP_PROTEIN_LOCALIZATION_TO_GOLGI_APPARATUS, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_EMBRYO_DEVELOPMENT, GOBP_RETROGRADE_TRANSPORT_ENDOSOME_TO_GOLGI, GOBP_LOCALIZATION_WITHIN_MEMBRANE

GO Biological Process (6): intracellular protein transport (GO:0006886), signal transduction (GO:0007165), gastrulation (GO:0007369), protein localization to Golgi apparatus (GO:0034067), retrograde transport, endosome to Golgi (GO:0042147), Golgi to plasma membrane protein transport (GO:0043001)

GO Molecular Function (4): GTPase activity (GO:0003924), GTP binding (GO:0005525), nucleotide binding (GO:0000166), protein binding (GO:0005515)

GO Cellular Component (5): Golgi apparatus (GO:0005794), trans-Golgi network (GO:0005802), cytosol (GO:0005829), membrane (GO:0016020), trans-Golgi network membrane (GO:0032588)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Intra-Golgi and retrograde Golgi-to-ER traffic	1
Vesicle-mediated transport	1
Membrane Trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein transport	2
cytoplasm	2
cellular anatomical structure	2
intracellular protein localization	1
intracellular transport	1
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
ectoderm formation	1
endoderm formation	1
mesoderm formation	1
embryonic morphogenesis	1
protein localization to organelle	1
intercellular transport	1
endosomal transport	1
cytosolic transport	1
Golgi to plasma membrane transport	1
establishment of protein localization to plasma membrane	1
protein localization to plasma membrane	1
ribonucleoside triphosphate phosphatase activity	1
guanyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
binding	1
endomembrane system	1
intracellular membrane-bounded organelle	1
Golgi apparatus subcompartment	1
trans-Golgi network	1
organelle membrane	1

Protein interactions and networks

STRING

1438 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARFRP1	SYS1	Q8N2H4	962
ARFRP1	ZGPAT	Q8N5A5	622
ARFRP1	CDKN2A	P42771	613
ARFRP1	GMEB2	Q9UKD1	597
ARFRP1	KPNA2	P52292	590
ARFRP1	SCOC	Q9UIL1	505
ARFRP1	JDP2	Q8WYK2	494
ARFRP1	FNDC11	Q9BVV2	494
ARFRP1	GBF1	Q92538	490
ARFRP1	GOLGA1	Q92805	482
ARFRP1	VPS53	Q5VIR6	481
ARFRP1	GRIP1	Q9Y3R0	479
ARFRP1	GOLGA4	Q13439	478
ARFRP1	STMN3	Q9NZ72	472
ARFRP1	NAA30	Q147X3	472

IntAct

23 interactions, top by confidence:

A	B	Type	Score
GLP1R	ARFRP1	psi-mi:“MI:0915”(physical association)	0.370
PB2		psi-mi:“MI:0914”(association)	0.350
	HLA-C	psi-mi:“MI:0914”(association)	0.350
CLTA	CLTB	psi-mi:“MI:0914”(association)	0.350
GPR107	JTB	psi-mi:“MI:0914”(association)	0.350
TMED10	PGRMC1	psi-mi:“MI:0914”(association)	0.350
SLC25A26	NBAS	psi-mi:“MI:0914”(association)	0.350
ARFRP1	PTPN11	psi-mi:“MI:2364”(proximity)	0.270
AKT1	ARFRP1	psi-mi:“MI:2364”(proximity)	0.270
BRAF	ARFRP1	psi-mi:“MI:2364”(proximity)	0.270
FBXW7	ARFRP1	psi-mi:“MI:2364”(proximity)	0.270
SMAD4	ARFRP1	psi-mi:“MI:2364”(proximity)	0.270
SPOP	ARFRP1	psi-mi:“MI:2364”(proximity)	0.270
ARFRP1	EGFR	psi-mi:“MI:2364”(proximity)	0.270
ARFRP1	TP53	psi-mi:“MI:2364”(proximity)	0.270
ARFRP1	PTEN	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (32): ARFRP1 (Two-hybrid), ARFRP1 (Affinity Capture-RNA), AP1G1 (Reconstituted Complex), AP1M1 (Reconstituted Complex), VANGL2 (Reconstituted Complex), ARFRP1 (Proximity Label-MS), ARFRP1 (Affinity Capture-RNA), ARFRP1 (Reconstituted Complex), ARFRP1 (Negative Genetic), ARFRP1 (Negative Genetic), ARFRP1 (Affinity Capture-MS), ARFRP1 (Affinity Capture-MS), ARFRP1 (Affinity Capture-MS), LEMD3 (Proximity Label-MS), CCT8 (Proximity Label-MS)

ESM2 similar proteins: A1CRG9, A1D4D1, A3LTA2, A5DR82, A5E5G3, O04266, O04267, O04834, P0C583, P0C950, P0C951, P0CR30, P0CR31, P0CT16, P0CT17, P20606, P36536, P52884, P78976, Q01474, Q01475, Q02804, Q0CUN7, Q0UKC0, Q13795, Q23445, Q2HA55, Q3T0D7, Q3T0T7, Q4P0I7, Q4WJS7, Q52NJ3, Q559R0, Q59S78, Q5BGB9, Q5HZY2, Q5PYH3, Q5R548, Q5R579, Q6BVA7

Diamond homologs: A8INQ0, A8ISN6, B5FYQ0, O04266, O04834, O08697, O23778, O45379, O48649, O48920, P0CM16, P0CM17, P0DH91, P11076, P19146, P20606, P22274, P26990, P26991, P36397, P36404, P36405, P36579, P37996, P38116, P40616, P40940, P40945, P40946, P49076, P51643, P51645, P51821, P51822, P51823, P51824, P61204, P61205, P61206, P61207

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	37
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
979738	GRCh37/hg19 20q13.33(chr20:61975605-62915555)x1	Pathogenic

SpliceAI

2316 predictions. Top by Δscore:

Variant	Effect	Δscore
20:63700597:CTCA:C	donor_loss	1.0000
20:63700598:TCA:T	donor_loss	1.0000
20:63700599:CACC:C	donor_loss	1.0000
20:63700600:AC:A	donor_gain	1.0000
20:63700600:ACCC:A	donor_loss	1.0000
20:63700601:CC:C	donor_gain	1.0000
20:63700698:CACGT:C	acceptor_gain	1.0000
20:63700700:CGT:C	acceptor_gain	1.0000
20:63700702:TCTG:T	acceptor_loss	1.0000
20:63700703:C:CC	acceptor_gain	1.0000
20:63700703:CTG:C	acceptor_loss	1.0000
20:63702130:ACTC:A	donor_loss	1.0000
20:63702131:CTCA:C	donor_loss	1.0000
20:63702132:TCACC:T	donor_loss	1.0000
20:63702133:CACCA:C	donor_loss	1.0000
20:63702134:A:AC	donor_gain	1.0000
20:63702135:C:CC	donor_gain	1.0000
20:63702135:CCAAA:C	donor_gain	1.0000
20:63702213:TAATA:T	acceptor_gain	1.0000
20:63702214:AATA:A	acceptor_gain	1.0000
20:63702215:ATA:A	acceptor_gain	1.0000
20:63702216:TA:T	acceptor_gain	1.0000
20:63702216:TACT:T	acceptor_loss	1.0000
20:63702217:ACTG:A	acceptor_loss	1.0000
20:63702218:C:CC	acceptor_gain	1.0000
20:63702219:T:A	acceptor_loss	1.0000
20:63705172:A:C	donor_gain	1.0000
20:63706436:CCGA:C	acceptor_gain	1.0000
20:63706437:CGA:C	acceptor_gain	1.0000
20:63706437:CGAC:C	acceptor_gain	1.0000

AlphaMissense

1305 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:63701842:C:A	K135N	0.999
20:63701842:C:G	K135N	0.999
20:63706397:T:G	D75A	0.999
20:63707007:C:A	G29W	0.999
20:63702198:C:T	G95D	0.998
20:63706363:C:A	W86C	0.998
20:63706363:C:G	W86C	0.998
20:63706365:A:G	W86R	0.998
20:63706365:A:T	W86R	0.998
20:63706397:T:C	D75G	0.998
20:63706398:C:G	D75H	0.998
20:63706656:A:G	L59P	0.998
20:63707002:C:A	K30N	0.998
20:63707002:C:G	K30N	0.998
20:63707003:T:A	K30M	0.998
20:63707004:T:G	K30Q	0.998
20:63707006:C:T	G29E	0.998
20:63707022:C:G	G24R	0.998
20:63701843:T:A	K135M	0.997
20:63701843:T:G	K135T	0.997
20:63701844:T:C	K135E	0.997
20:63701845:G:C	N134K	0.997
20:63701845:G:T	N134K	0.997
20:63706397:T:A	D75V	0.997
20:63706659:C:T	G58D	0.997
20:63706660:C:G	G58R	0.997
20:63706665:G:A	T56I	0.997
20:63707006:C:A	G29V	0.997
20:63707007:C:G	G29R	0.997
20:63707007:C:T	G29R	0.997

dbSNP variants (sampled 300 via entrez): RS1000273367 (20:63699173 T>G), RS1000306698 (20:63701594 G>A), RS1000436195 (20:63704537 A>G), RS1000445426 (20:63706232 C>T), RS1000563134 (20:63705472 A>G), RS1000780554 (20:63705231 G>A), RS1000918676 (20:63706149 C>T), RS1001128062 (20:63701745 G>A), RS1001352045 (20:63709836 C>G), RS1001357116 (20:63701323 G>A), RS1001414186 (20:63701972 T>G), RS1001515087 (20:63698801 C>G), RS1001735960 (20:63698991 C>T), RS1001824618 (20:63701558 C>T), RS1001842434 (20:63698197 G>A)

Disease associations

OMIM: gene MIM:604699 | disease phenotypes: MIM:615190

GenCC curated gene-disease

Mondo (1): dyskeratosis congenita, autosomal recessive 5 (MONDO:0014076)

Orphanet (0):

HPO phenotypes

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

GWAS associations

13 associations (top):

Study	Trait	p-value
GCST001942_22	Prostate cancer	4.000000e-16
GCST004131_34	Inflammatory bowel disease	3.000000e-26
GCST004132_110	Crohn’s disease	3.000000e-13
GCST004133_15	Ulcerative colitis	9.000000e-17
GCST007344_18	Estimated glomerular filtration rate	2.000000e-08
GCST007563_15	Allergic disease (asthma, hay fever or eczema)	3.000000e-08
GCST007564_6	Asthma or allergic disease (pleiotropy)	3.000000e-10
GCST008916_69	Asthma	3.000000e-09
GCST010002_71	Refractive error	1.000000e-14
GCST011320_35	Type 2 diabetes or prostate cancer (pleiotropy)	2.000000e-13
GCST90002379_166	Basophil count	6.000000e-09
GCST90002380_24	Basophil percentage of white cells	6.000000e-10
GCST90002402_603	Platelet count	2.000000e-15

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0005090	basophil count
EFO:0007992	basophil percentage of leukocytes
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
Valproic Acid	decreases expression, increases methylation	2
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	affects splicing	1
beta-lapachone	increases expression	1
cobaltous chloride	decreases expression	1
manganese chloride	decreases expression, increases abundance, affects cotreatment	1
ferrous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Fulvestrant	increases methylation	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	affects cotreatment, increases expression	1
Formaldehyde	decreases expression	1
Manganese	decreases expression, increases abundance, affects cotreatment	1
Selenium	increases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Urethane	decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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