ARID5A

Summary

ARID5A (AT-rich interaction domain 5A, HGNC:17361) is a protein-coding gene on chromosome 2q11.2, encoding AT-rich interactive domain-containing protein 5A (Q03989). DNA-binding protein that may regulate transcription and act as a repressor by binding to AT-rich stretches in the promoter region of target genes.

Members of the ARID protein family, including ARID5A, have diverse functions but all appear to play important roles in development, tissue-specific gene expression, and regulation of cell growth (Patsialou et al., 2005 [PubMed 15640446]).

Source: NCBI Gene 10865 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 106 total — 2 pathogenic
• Phenotypes (HPO): 1
• MANE Select transcript: NM_212481

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17361
Approved symbol	ARID5A
Name	AT-rich interaction domain 5A
Location	2q11.2
Locus type	gene with protein product
Status	Approved
Aliases	MRF-1, RP11-363D14
Ensembl gene	ENSG00000196843
Ensembl biotype	protein_coding
OMIM	611583
Entrez	10865

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 8 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000357485, ENST00000412735, ENST00000454558, ENST00000467498, ENST00000470579, ENST00000497920, ENST00000673792, ENST00000858788, ENST00000858789, ENST00000858790, ENST00000921872, ENST00000969939

RefSeq mRNA: 7 — MANE Select: NM_212481 NM_001319085, NM_001319087, NM_001319092, NM_001319093, NM_001319094, NM_001319096, NM_212481

CCDS: CCDS33251, CCDS82484

Canonical transcript exons

ENST00000357485 — 7 exons

Exon	Start	End
ENSE00001762064	96536752	96536830
ENSE00003465058	96549321	96549459
ENSE00003480868	96549753	96549805
ENSE00003513833	96550574	96550733
ENSE00003543381	96550188	96550285
ENSE00003612907	96551099	96552634
ENSE00003673503	96547402	96547517

Expression profiles

Bgee: expression breadth ubiquitous, 258 present calls, max score 97.97.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.6999 / max 1003.3600, expressed in 1789 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
21470	27.4278	1749
21469	1.6363	938
21471	0.8953	156
21472	0.6109	223
21473	0.1296	56

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of stomach	UBERON:0001199	97.97	gold quality
ascending aorta	UBERON:0001496	97.27	gold quality
thoracic aorta	UBERON:0001515	97.14	gold quality
aorta	UBERON:0000947	96.37	gold quality
descending thoracic aorta	UBERON:0002345	96.23	gold quality
popliteal artery	UBERON:0002250	95.87	gold quality
tibial artery	UBERON:0007610	95.85	gold quality
left uterine tube	UBERON:0001303	95.45	gold quality
granulocyte	CL:0000094	95.40	gold quality
vena cava	UBERON:0004087	94.68	gold quality
left coronary artery	UBERON:0001626	94.37	gold quality
omental fat pad	UBERON:0010414	94.32	gold quality
peritoneum	UBERON:0002358	94.28	gold quality
right lung	UBERON:0002167	94.03	gold quality
saphenous vein	UBERON:0007318	94.02	gold quality
coronary artery	UBERON:0001621	93.76	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	93.38	gold quality
adipose tissue of abdominal region	UBERON:0007808	93.09	gold quality
lower esophagus muscularis layer	UBERON:0035833	92.80	gold quality
apex of heart	UBERON:0002098	92.79	gold quality
lower esophagus	UBERON:0013473	92.71	gold quality
body of uterus	UBERON:0009853	92.49	gold quality
upper lobe of left lung	UBERON:0008952	92.09	gold quality
blood	UBERON:0000178	91.91	gold quality
right coronary artery	UBERON:0001625	91.91	gold quality
hindlimb stylopod muscle	UBERON:0004252	91.80	gold quality
spleen	UBERON:0002106	91.60	gold quality
right atrium auricular region	UBERON:0006631	91.23	gold quality
muscle layer of sigmoid colon	UBERON:0035805	90.97	gold quality
type B pancreatic cell	CL:0000169	90.81	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-MTAB-8142	yes	133.13
E-HCAD-8	yes	71.37
E-CURD-88	yes	36.57
E-HCAD-4	yes	21.33
E-HCAD-11	yes	20.74
E-GEOD-110499	no	719.69
E-CURD-112	no	3.51
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

4 targets.

Target	Regulation
COL2A1
ESR1
MBP
SRSF2

Upstream regulators (CollecTRI, top): STAT3

miRNA regulators (miRDB)

18 targeting ARID5A, 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-4778-3P	99.93	70.40	1818
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-3156-3P	99.76	66.72	939
HSA-MIR-4690-5P	99.65	66.24	813
HSA-MIR-5004-3P	99.54	68.27	1371
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-6165	99.44	67.12	1389
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-6510-5P	99.14	66.59	1081
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-6882-3P	98.23	67.01	1119
HSA-MIR-6742-3P	97.95	64.50	1490
HSA-MIR-6726-5P	95.97	63.72	841
HSA-MIR-920	95.97	63.95	811
HSA-MIR-4300	95.85	64.56	1003
HSA-MIR-5591-5P	95.85	64.76	1002
HSA-MIR-4745-3P	83.50	60.58	126

Literature-anchored findings (GeneRIF, showing 2)

• AT-rich-interactive domain-containing protein 5A functions as a negative regulator of retinoic acid receptor-related orphan nuclear receptor gammat-induced Th17 cell differentiation. (PMID:24782182)
• Overexpression of ARID5A resulted in more number of cells in G0/G1 phase of cell cycle (PMID:29044508)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Arid5a	ENSMUSG00000037447
rattus_norvegicus	Arid5a	ENSRNOG00000015382
drosophila_melanogaster	htk	FBGN0085451
caenorhabditis_elegans		WBGENE00044689

Paralogs (3): ARID4A (ENSG00000032219), ARID4B (ENSG00000054267), ARID5B (ENSG00000150347)

Protein

Protein identifiers

AT-rich interactive domain-containing protein 5A — Q03989 (reviewed: Q03989)

Alternative names: Modulator recognition factor 1

All UniProt accessions (3): A0A669KBH0, Q03989, F6Q9D3

UniProt curated annotations — full annotation on UniProt →

Function. DNA-binding protein that may regulate transcription and act as a repressor by binding to AT-rich stretches in the promoter region of target genes. May positively regulate chondrocyte-specific transcription such as of COL2A1 in collaboration with SOX9 and positively regulate histone H3 acetylation at chondrocyte-specific genes. May stimulate early-stage chondrocyte differentiation and inhibit later stage differention. Can repress ESR1-mediated transcriptional activation; proposed to act as corepressor for selective nuclear hormone receptors. As an RNA-binding protein, involved in the regulation of inflammatory response by stabilizing selective inflammation-related mRNAs, such as STAT3 and TBX21. Also stabilizes IL6 mRNA. Binds to stem loop structures located in the 3’UTRs of IL6, STAT3 and TBX21 mRNAs; at least for STAT3 prevents binding of ZC3H12A to the mRNA stem loop structure thus inhibiting its degradation activity. Contributes to elevated IL6 levels possibly implicated in autoimmunity processes. IL6-dependent stabilization of STAT3 mRNA may promote differentiation of naive CD4+ T-cells into T-helper Th17 cells. In CD4+ T-cells may also inhibit RORC-induced Th17 cell differentiation independently of IL6 signaling. Stabilization of TBX21 mRNA contributes to elevated interferon-gamma secretion in Th1 cells possibly implicated in the establishment of septic shock. Stabilizes TNFRSF4/OX40 mRNA by binding to the conserved stem loop structure in its 3’UTR; thereby competing with the mRNA-destabilizing functions of RC3H1 and endoribonuclease ZC3H12A.

Subunit / interactions. Interacts with SOX9. Interacts with ESR1. Interacts with RORC.

Subcellular location. Nucleus.

Post-translational modifications. Phosphorylated by MAPK14 on serine residues involving a TLR4 signaling pathway upon lipopolysaccharide (LPS) stimulation leading to its ubiquitination and proteasomal degradation. Ubiquitinated leading to proteasomal degradation; involving WWP1 linked to MAPK14-mediated phosphorylation upon LPS stimulation.

Isoforms (2)

UniProt ID	Names	Canonical?
Q03989-1	1	yes
Q03989-5	2

RefSeq proteins (7): NP_001306014, NP_001306016, NP_001306021, NP_001306022, NP_001306023, NP_001306025, NP_997646* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001606	ARID_dom	Domain
IPR036431	ARID_dom_sf	Homologous_superfamily
IPR051232	ARID/SWI1_ChromRemod	Family

Pfam: PF01388

UniProt features (18 total): modified residue 5, region of interest 5, cross-link 2, compositionally biased region 2, chain 1, domain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q03989-F1	55.26	0.10

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 (7): 256, 289, 438, 463, 85, 94, 23

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 354 (showing top): GOBP_POSITIVE_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, YAGI_AML_WITH_INV_16_TRANSLOCATION, GOBP_CARTILAGE_DEVELOPMENT, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, MODULE_255, GOBP_CELLULAR_RESPONSE_TO_LIPID, GOBP_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, ZHAN_MULTIPLE_MYELOMA_MF_UP, GCANCTGNY_MYOD_Q6, GOBP_CELLULAR_RESPONSE_TO_BIOTIC_STIMULUS, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_3_UTR_MEDIATED_MRNA_STABILIZATION, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, MODULE_317

GO Biological Process (16): negative regulation of transcription by RNA polymerase II (GO:0000122), chondrocyte differentiation (GO:0002062), regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of type II interferon production (GO:0032729), positive regulation of interleukin-17 production (GO:0032740), positive regulation of interleukin-6 production (GO:0032755), positive regulation of tumor necrosis factor production (GO:0032760), innate immune response (GO:0045087), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of transcription by RNA polymerase II (GO:0045944), cellular response to lipopolysaccharide (GO:0071222), cellular response to estrogen stimulus (GO:0071391), positive regulation of 3’-UTR-mediated mRNA stabilization (GO:1905870), positive regulation of T-helper 17 type immune response (GO:2000318), positive regulation of T-helper 1 cell cytokine production (GO:2000556), immune system process (GO:0002376)

GO Molecular Function (15): transcription cis-regulatory region binding (GO:0000976), DNA binding (GO:0003677), chromatin binding (GO:0003682), transcription corepressor activity (GO:0003714), transcription factor binding (GO:0008134), nuclear estrogen receptor binding (GO:0030331), RNA stem-loop binding (GO:0035613), mRNA 3’-UTR AU-rich region binding (GO:0035925), identical protein binding (GO:0042802), sequence-specific DNA binding (GO:0043565), nuclear retinoid X receptor binding (GO:0046965), nuclear thyroid hormone receptor binding (GO:0046966), nuclear androgen receptor binding (GO:0050681), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), transcription regulator complex (GO:0005667), nucleolus (GO:0005730)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transcription by RNA polymerase II	3
positive regulation of cytokine production	3
nuclear receptor binding	3
regulation of transcription by RNA polymerase II	2
negative regulation of DNA-templated transcription	2
regulation of DNA-templated transcription	2
nucleic acid binding	2
binding	2
protein binding	2
nuclear lumen	2
cell differentiation	1
cartilage development	1
type II interferon production	1
regulation of type II interferon production	1
interleukin-17 production	1
regulation of interleukin-17 production	1
interleukin-6 production	1
regulation of interleukin-6 production	1
tumor necrosis factor production	1
regulation of tumor necrosis factor production	1
positive regulation of tumor necrosis factor superfamily cytokine production	1
immune response	1
defense response to symbiont	1
DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
positive regulation of DNA-templated transcription	1
response to lipopolysaccharide	1
cellular response to molecule of bacterial origin	1
cellular response to lipid	1
cellular response to oxygen-containing compound	1
cellular response to hormone stimulus	1
response to estrogen	1
positive regulation of gene expression	1
3’-UTR-mediated mRNA stabilization	1
regulation of 3’-UTR-mediated mRNA stabilization	1
positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	1
T-helper 17 type immune response	1
regulation of T-helper 17 type immune response	1
positive regulation of T cell cytokine production	1
positive regulation of T-helper 1 type immune response	1

Protein interactions and networks

STRING

1234 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARID5A	KDM5C	P41229	691
ARID5A	ZC3H12A	Q5D1E8	613
ARID5A	RBL2	Q08999	588
ARID5A	ARID3B	Q8IVW6	572
ARID5A	SAP30	O75446	548
ARID5A	ARID4A	P29374	521
ARID5A	TRAF5	O00463	517
ARID5A	RC3H1	Q5TC82	506
ARID5A	ARID3A	Q99856	503
ARID5A	SOX9	P48436	499
ARID5A	ING2	Q9H160	491
ARID5A	KDM5B	Q9UGL1	482
ARID5A	NUFIP2	Q7Z417	462
ARID5A	SBNO2	Q9Y2G9	455
ARID5A	ESR2	Q92731	434

IntAct

394 interactions, top by confidence:

A	B	Type	Score
KRTAP12-2	ARID5A	psi-mi:“MI:0915”(physical association)	0.700
ARID5A	DAZAP2	psi-mi:“MI:0915”(physical association)	0.700
ARID5A	PNMA1	psi-mi:“MI:0915”(physical association)	0.700
ARID5A	MDFI	psi-mi:“MI:0915”(physical association)	0.700
CKS1B	ARID5A	psi-mi:“MI:0915”(physical association)	0.700
ARID5A	KRTAP12-2	psi-mi:“MI:0915”(physical association)	0.700
DAZAP2	ARID5A	psi-mi:“MI:0915”(physical association)	0.700
ARID5A	CKS1B	psi-mi:“MI:0915”(physical association)	0.700
ARID5A	ESR1	psi-mi:“MI:0915”(physical association)	0.630
ESR1	ARID5A	psi-mi:“MI:0915”(physical association)	0.630
ARID5A	KRTAP8-1	psi-mi:“MI:0915”(physical association)	0.560
ARID5A	BOLL	psi-mi:“MI:0915”(physical association)	0.560
ARID5A	SOX5	psi-mi:“MI:0915”(physical association)	0.490
KRTAP12-4	ARID5A	psi-mi:“MI:0915”(physical association)	0.490
GOLGA2	ARID5A	psi-mi:“MI:0915”(physical association)	0.490
ARID5A	KRT40	psi-mi:“MI:0915”(physical association)	0.490
RBPMS	ARID5A	psi-mi:“MI:0915”(physical association)	0.490
ARID5A	RHOXF2	psi-mi:“MI:0915”(physical association)	0.490

BioGRID (150): ARID5A (Two-hybrid), ARID5A (Two-hybrid), ARID5A (Two-hybrid), ARID5A (Two-hybrid), ARID5A (Two-hybrid), ARID5A (Two-hybrid), ARID5A (Two-hybrid), RBPMS (Two-hybrid), RHOXF2 (Two-hybrid), KRT40 (Two-hybrid), KRTAP12-2 (Two-hybrid), KRTAP12-4 (Two-hybrid), ARID5A (Two-hybrid), SOX5 (Two-hybrid), ARID5A (Two-hybrid)

ESM2 similar proteins: A2VDR9, A5PKG8, A6NMT0, A7MB40, A8MUI8, E2R9X2, O00257, O15353, O43151, O55187, P19419, P30658, P48382, P52950, P59598, Q03989, Q0GGX2, Q13029, Q14781, Q28BT7, Q2MHN3, Q32MQ0, Q32N19, Q3SWY1, Q3TEI4, Q3U108, Q3UHR0, Q497V6, Q568E2, Q571I4, Q5JPB2, Q5NSW5, Q5TGY3, Q61818, Q6PAL7, Q6ZRI6, Q7TSH3, Q7Z5J4, Q811R2, Q86YN6

Diamond homologs: A2BEA6, A2BH40, A2CG63, A6NKF2, A6PWV5, E1BLP6, E2R9X2, E7F888, E9Q4N7, F8VPQ2, O02326, O14497, O74365, P29374, P29375, P41229, P41230, Q03214, Q03989, Q14865, Q24573, Q30DN6, Q38JA7, Q3SWY1, Q3U108, Q3UXZ9, Q4H3P5, Q4LE39, Q5F3R2, Q5XGD9, Q5XUN4, Q5ZJ69, Q62431, Q6GQD7, Q6IQX0, Q8BM75, Q8IN94, Q8IVW6, Q8MQH7, Q8NFD5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 122 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
SUMOylation of intracellular receptors	5	26.7×	1e-04
Nuclear Receptor transcription pathway	6	19.1×	1e-04
Keratinization	15	13.3×	1e-10

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	93
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
3024612	GRCh37/hg19 2q11.1-11.2(chr2:96780545-98098961)x1	Pathogenic
3248883	NC_000002.12:g.(?96274999)(96809530_?)del	Pathogenic

SpliceAI

1279 predictions. Top by Δscore:

Variant	Effect	Δscore
2:96547396:TTGCA:T	acceptor_loss	1.0000
2:96547397:TGCA:T	acceptor_loss	1.0000
2:96547398:GCA:G	acceptor_loss	1.0000
2:96547399:CAG:C	acceptor_loss	1.0000
2:96547400:A:AG	acceptor_gain	1.0000
2:96547400:A:AT	acceptor_loss	1.0000
2:96547401:G:GT	acceptor_gain	1.0000
2:96547401:GC:G	acceptor_gain	1.0000
2:96547401:GCA:G	acceptor_gain	1.0000
2:96547401:GCAG:G	acceptor_loss	1.0000
2:96547401:GCAGC:G	acceptor_gain	1.0000
2:96547514:GGAG:G	donor_gain	1.0000
2:96547515:GAG:G	donor_gain	1.0000
2:96547515:GAGG:G	donor_gain	1.0000
2:96547518:G:C	donor_loss	1.0000
2:96547518:G:GG	donor_gain	1.0000
2:96547519:T:G	donor_loss	1.0000
2:96549319:A:AG	acceptor_gain	1.0000
2:96549320:G:GA	acceptor_loss	1.0000
2:96549320:G:GG	acceptor_gain	1.0000
2:96549320:GGACT:G	acceptor_gain	1.0000
2:96549455:GCAGA:G	donor_gain	1.0000
2:96549458:GA:G	donor_gain	1.0000
2:96549460:G:GG	donor_gain	1.0000
2:96549751:A:AG	acceptor_gain	1.0000
2:96549751:A:AT	acceptor_loss	1.0000
2:96549752:G:GT	acceptor_gain	1.0000
2:96549752:GT:G	acceptor_gain	1.0000
2:96549752:GTT:G	acceptor_gain	1.0000
2:96549752:GTTA:G	acceptor_gain	1.0000

AlphaMissense

3856 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:96549381:T:C	F61L	1.000
2:96549382:T:C	F61S	1.000
2:96549383:C:A	F61L	1.000
2:96549383:C:G	F61L	1.000
2:96549402:T:C	F68L	1.000
2:96549403:T:C	F68S	1.000
2:96549404:C:A	F68L	1.000
2:96549404:C:G	F68L	1.000
2:96549407:G:A	M69I	1.000
2:96549407:G:C	M69I	1.000
2:96549407:G:T	M69I	1.000
2:96549427:T:A	I76N	1.000
2:96549450:T:C	F84L	1.000
2:96549451:T:C	F84S	1.000
2:96549452:C:A	F84L	1.000
2:96549452:C:G	F84L	1.000
2:96549455:G:C	K85N	1.000
2:96549455:G:T	K85N	1.000
2:96550206:T:A	W111R	1.000
2:96550206:T:C	W111R	1.000
2:96550207:G:C	W111S	1.000
2:96550208:G:C	W111C	1.000
2:96550208:G:T	W111C	1.000
2:96550251:A:C	S126R	1.000
2:96550253:C:A	S126R	1.000
2:96550253:C:G	S126R	1.000
2:96550258:C:A	A128D	1.000
2:96550263:T:C	C130R	1.000
2:96550265:C:G	C130W	1.000
2:96550269:C:A	R132S	1.000

dbSNP variants (sampled 300 via entrez): RS1000175742 (2:96540594 A>G), RS1000288922 (2:96548073 G>A), RS1000671272 (2:96541133 G>A), RS1000679103 (2:96549115 C>A), RS1000780105 (2:96547862 C>A,T), RS1001030173 (2:96549482 G>A), RS1001030287 (2:96536170 T>G), RS1001213923 (2:96547605 C>A,G), RS1001392403 (2:96548411 ATGCACTACCAGGCC>A), RS1001465903 (2:96540706 A>G), RS1001495609 (2:96540418 C>T), RS1001583084 (2:96541787 G>A), RS1001635348 (2:96541319 T>G), RS1001799491 (2:96548497 C>T), RS1001856233 (2:96552677 G>GGCA)

Disease associations

OMIM: gene MIM:611583 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): inherited retinal dystrophy (MONDO:0019118)

Orphanet (1): OBSOLETE: Inherited retinal disorder (Orphanet:71862)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0000556	Retinal dystrophy

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST000857_1	Event-related brain oscillations	4.000000e-06
GCST004600_71	Eosinophil percentage of white cells	7.000000e-39
GCST004606_60	Eosinophil count	8.000000e-39
GCST90002381_35	Eosinophil count	2.000000e-43
GCST90002382_42	Eosinophil percentage of white cells	2.000000e-44

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004358	event-related brain oscillation
EFO:0007991	eosinophil percentage of leukocytes
EFO:0004842	eosinophil count

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D058499	Retinal Dystrophies	C11.768.585.658

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	2
Estradiol	decreases reaction, increases activity, increases expression	2
Nickel	increases expression	2
aristolochic acid I	increases expression	1
FR900359	increases phosphorylation	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
alpha-pinene	decreases expression, increases abundance, affects cotreatment	1
mono-(2-ethylhexyl)phthalate	decreases methylation, increases abundance	1
afimoxifene	decreases reaction, increases activity	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
pentanal	increases expression	1
15-acetyldeoxynivalenol	increases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
bisphenol S	affects cotreatment, increases expression	1
jinfukang	increases expression	1
Sunitinib	decreases expression	1
Acrolein	affects cotreatment, decreases expression, increases abundance	1
Air Pollutants	affects cotreatment, decreases expression, increases abundance	1
Amiodarone	increases expression	1
Atrazine	increases expression	1
Caffeine	increases phosphorylation	1
Dexamethasone	affects cotreatment, increases expression	1
Diethylhexyl Phthalate	increases abundance, decreases methylation	1
Indomethacin	affects cotreatment, increases expression	1
Melphalan	increases expression	1
Ozone	affects cotreatment, decreases expression, increases abundance	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04224207	PHASE3	COMPLETED	Management of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT07082855	PHASE3	NOT_YET_RECRUITING	A Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT03763227	PHASE2	COMPLETED	Intravitreal Ranibizumab (Lucentis®) in the Treatment of Non-leaking Macular Cysts in Retinal Dystrophy
NCT04068207	PHASE2	COMPLETED	Minocycline Treatment in Retinitis Pigmentosa
NCT04945772	PHASE2	COMPLETED	Efficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT05902962	PHASE1	COMPLETED	SAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects
NCT06319872	PHASE1	RECRUITING	The Effects of Disulfiram (Antabuse®) on Visual Acuity in Patients With Retinal Degeneration
NCT06455826	PHASE1	COMPLETED	MAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects (Wallaby)
NCT04855045	PHASE2/PHASE3	UNKNOWN	An Open-label, Dose Escalation and Double-masked, Randomized, Controlled Trial Evaluating Safety and Tolerability of Sepofarsen in Children (<8 Years of Age) With LCA10 Caused by Mutations in the CEP290 Gene.
NCT03872479	PHASE1/PHASE2	UNKNOWN	Single Ascending Dose Study in Participants With LCA10
NCT04123626	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	A Study to Evaluate the Safety and Tolerability of QR-1123 in Subjects With Autosomal Dominant Retinitis Pigmentosa Due to the P23H Mutation in the RHO Gene
NCT04545736	PHASE1/PHASE2	RECRUITING	Oral Metformin for Treatment of ABCA4 Retinopathy
NCT06212297	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	Fellow-eye Study (FE) of LX101 in Subjects With Inherited Retinal Dystrophy
NCT06852963	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	A Repeat-Dose, Open-Label, Two Arm Safety and Efficacy Study of Two Doses of VP-001 Administered Intravitreally in Participants With Confirmed PRPF31 Mutation-Associated Retinal Dystrophy, Including Participants Previously Treated With VP001
NCT07177196	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	Personalized Antisense Oligonucleotide Therapy for a Single Participant With PRPH2 Mutation Associated With Retinal Dystrophy
NCT07063030	EARLY_PHASE1	RECRUITING	A Study of LX107 Gene Therapy in AIPL1-IRD Patients
NCT01546181	Not specified	COMPLETED	Retinal Imaging by Adaptive Optics in Healthy Eyes and During Retinal and General Diseases
NCT01876147	Not specified	COMPLETED	Visual and Functional Assessment in Low Vision Patients
NCT01920867	Not specified	UNKNOWN	Stem Cell Ophthalmology Treatment Study
NCT02014389	Not specified	RECRUITING	Evaluation of Objective Perimetry Using Chromatic Multifocal Pupillometer
NCT02983305	Not specified	COMPLETED	Optical Head-Mounted Display Technology for Low Vision Rehabilitation
NCT03592017	Not specified	COMPLETED	Performance of Long-wavelength Autofluorescence Imaging
NCT03662386	Not specified	TERMINATED	Prospective Analysis of Genotype-phenotype Correlations Observed in a Large Cohort of Patients With Hereditary Retinal Dystrophies - GEPHIRD
NCT03691168	Not specified	UNKNOWN	Multi-center Observation of the Natural Course of Inherited Retinal Dystrophies
NCT03843840	Not specified	COMPLETED	Dual Wavelength OCT
NCT03853252	Not specified	COMPLETED	iPS Cells of Patients for Models of Retinal Dystrophies
NCT05130385	Not specified	UNKNOWN	High Resolution Optical Coherence Tomography
NCT05294978	Not specified	RECRUITING	EyeConic: Qualification for Cone-Optogenetics
NCT05573984	Not specified	ACTIVE_NOT_RECRUITING	Natural History of PRPF31 Mutation-Associated Retinal Dystrophy
NCT05793515	Not specified	COMPLETED	Mechanisms of Inherited Retinal Dystrophies Using Whole Genome Sequencing and in Vitro and in Vivo Models
NCT05820100	Not specified	COMPLETED	Observational Study to Assess the Reliability and Validity of the MLYMT and MLSDT
NCT05976139	Not specified	RECRUITING	Micropulsed Laser in Patients With Macular Oedema in Retinal Dystrophies
NCT06162585	Not specified	ACTIVE_NOT_RECRUITING	Non-Interventional Long Term Follow-up Study of Participants Previously Enrolled in the RESTORE Study
NCT06177977	Not specified	RECRUITING	SS-HH-OCT as a Novel Diagnostic Modality for Early-Onset Retinal Dystrophies (EORDs)
NCT06375239	Not specified	RECRUITING	Observational Study to Assess Endpoint Operational Feasibility & Measurement Properties in Patients with Retinal Degeneration
NCT06908161	Not specified	NOT_YET_RECRUITING	Functional Assessments in Vision Impairment
NCT07085533	Not specified	RECRUITING	Natural History Study of Inherited Retinal Diseases
NCT07502664	Not specified	RECRUITING	Development and Evaluation of Functional Visual Field and Navigation Endpoints in Moderate to Profound Inherited Retinal Disease (DEFINE-IRD)
NCT07529041	Not specified	ENROLLING_BY_INVITATION	Real-time Acoustic Biofeedback for Enhancing Fixation Stability: A Proof-of-concept Study to Improve Ophthalmic Imaging Diagnostic Quality