KIAA1549

Summary

KIAA1549 (HGNC:22219) is a protein-coding gene on chromosome 7q34, encoding UPF0606 protein KIAA1549 (Q9HCM3). May play a role in photoreceptor function.

The protein encoded by this gene belongs to the UPF0606 family. This gene has been found to be fused to the BRAF oncogene in many cases of pilocytic astrocytoma. The fusion results from 2Mb tandem duplications at 7q34. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 57670 — RefSeq curated summary.

At a glance

• Gene–disease (curated): retinitis pigmentosa 86 (Strong, ClinGen) — +1 more curated relationship
• GWAS associations: 1
• Clinical variants (ClinVar): 1,604 total — 3 pathogenic, 4 likely-pathogenic
• Phenotypes (HPO): 37
• MANE Select transcript: NM_001164665

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22219
Approved symbol	KIAA1549
Name	KIAA1549
Location	7q34
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000122778
Ensembl biotype	protein_coding
OMIM	613344
Entrez	57670

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000422774, ENST00000440172, ENST00000924634, ENST00000924635, ENST00000948657, ENST00000948658

RefSeq mRNA: 2 — MANE Select: NM_001164665 NM_001164665, NM_020910

CCDS: CCDS47723, CCDS56513

Canonical transcript exons

ENST00000422774 — 20 exons

Exon	Start	End
ENSE00000000219	138981083	138981389
ENSE00000833424	138840133	138840278
ENSE00000833431	138905022	138905081
ENSE00001088064	138861139	138861456
ENSE00001088065	138881388	138881584
ENSE00001088066	138844317	138844474
ENSE00001088067	138871157	138871362
ENSE00001088069	138898955	138899132
ENSE00001088071	138867975	138868128
ENSE00001088072	138869538	138869761
ENSE00001088073	138894342	138894526
ENSE00001088074	138879538	138879653
ENSE00001088075	138852223	138852269
ENSE00001088261	138912372	138912460
ENSE00001088264	138911146	138911323
ENSE00001088267	138908991	138909121
ENSE00001088270	138906919	138907102
ENSE00001138356	138903588	138903736
ENSE00001613846	138831381	138838160
ENSE00001737714	138916748	138919438

Expression profiles

Bgee: expression breadth ubiquitous, 200 present calls, max score 90.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.8410 / max 312.9231, expressed in 1272 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
86471	4.1330	1232
86472	0.3030	149
86470	0.1766	64
86469	0.1631	49
86473	0.0653	18

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	90.56	gold quality
ganglionic eminence	UBERON:0004023	85.39	gold quality
ventricular zone	UBERON:0003053	83.58	gold quality
Brodmann (1909) area 23	UBERON:0013554	83.42	gold quality
middle temporal gyrus	UBERON:0002771	81.58	gold quality
seminal vesicle	UBERON:0000998	80.18	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.41	gold quality
stromal cell of endometrium	CL:0002255	78.52	gold quality
endothelial cell	CL:0000115	77.98	silver quality
Brodmann (1909) area 46	UBERON:0006483	77.98	gold quality
superior frontal gyrus	UBERON:0002661	76.94	gold quality
kidney epithelium	UBERON:0004819	76.70	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.43	gold quality
buccal mucosa cell	CL:0002336	76.01	gold quality
postcentral gyrus	UBERON:0002581	75.50	gold quality
entorhinal cortex	UBERON:0002728	75.03	gold quality
parietal lobe	UBERON:0001872	74.32	gold quality
secondary oocyte	CL:0000655	74.17	gold quality
primary visual cortex	UBERON:0002436	73.90	gold quality
epithelial cell of pancreas	CL:0000083	73.56	gold quality
oviduct epithelium	UBERON:0004804	73.50	gold quality
prefrontal cortex	UBERON:0000451	73.27	gold quality
sperm	CL:0000019	72.83	gold quality
frontal cortex	UBERON:0001870	72.52	gold quality
neocortex	UBERON:0001950	72.33	gold quality
occipital lobe	UBERON:0002021	72.33	gold quality
body of pancreas	UBERON:0001150	72.26	gold quality
pancreatic ductal cell	CL:0002079	72.17	silver quality
cartilage tissue	UBERON:0002418	71.86	gold quality
cerebral cortex	UBERON:0000956	71.78	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	14.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

295 targeting KIAA1549, 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-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790

Literature-anchored findings (GeneRIF, showing 14)

• KIAA1549 is a target gene of the BACH1 transcription factor according to ChIP-seq analysis in HEK 293 cells. (PMID:21555518)
• The frequency of BRAF-KIAA1549 fusion transcripts is significantly lower in adult patients with pilocytic astrocytoma. (PMID:21696415)
• KIAA1549:BRAF fusions predominate in pilocytic astrocytomas but are also present in some low-grade unclassifiable gliomas and glioneuronal tumors. (PMID:22157620)
• Our results suggest that in a small fraction of diffuse gliomas, KIAA1549-BRAF fusion gene and BRAF(v600E) mutation may be responsible for deregulation of the Ras-RAF-ERK signaling pathway (PMID:22591444)
• we found no cases of Rosette-forming glioneuronal tumors of the fourth ventricle showing KIAA1549-BRAF gene fusion or BRAF (V600E) mutation (PMID:22814862)
• Molecular genetic analysis revealed BRAF duplication and a KIAA1549-BRAF fusion gene in 82% of group II tumors, but in none of the group I tumors, and a BRAF:p.V600E mutation in 43% of group I tumors, but in none of the group II tumors. (PMID:24529209)
• we identify KIAA1549-BRAF gene fusions in 45 % of 82 low-grade glioma samples (PMID:24532263)
• Pediatric oligodendrogliomas (pODGs) can harbor the KIAA1549-BRAF fusion with aberrant MAPK/ERK signaling, and there exists an option of targeting these pathways in such patients. (PMID:25794445)
• This study confirmed the high frequency of KIAA1549:BRAF fusion in Pilocytic Astrocytomas. (PMID:26083571)
• Mutations in BRAF-KIAA1549 were associated with central nervous system tumors. (PMID:26115961)
• This study demonstrated that when whole chromosome 7 gain accompanies the KIAA1549-BRAF fusion, the fusion likely arises first. (PMID:26945035)
• these results demonstrate that f-BRAF expression creates a supportive tumor microenvironment through NFkappaB-mediated Ccl2 production and microglia recruitment. (PMID:30504064)
• Concomitant KIAA1549-BRAF fusion and IDH mutation in Pediatric spinal cord astrocytoma: a case report and literature review. (PMID:33641074)
• KIAA1549 promotes the development and chemoresistance of colorectal cancer by upregulating ERCC2. (PMID:37140813)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	D630045J12Rik	ENSMUSG00000063455
rattus_norvegicus	Kiaa1549	ENSRNOG00000013729

Paralogs (1): KIAA1549L (ENSG00000110427)

Protein

Protein identifiers

UPF0606 protein KIAA1549 — Q9HCM3 (reviewed: Q9HCM3)

All UniProt accessions (1): Q9HCM3

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in photoreceptor function.

Subcellular location. Membrane. Cell projection. Cilium.

Tissue specificity. Expression is low to moderate in retina and tissues, such as heart and kidney, and is predominantly expressed in brain. Abundantly expressed in the retina, compared with only minimal expression in brain and other tissues.

Post-translational modifications. O-glycosylated. O-mannosylated by POMT1 and POMT2 and elongated by POMGNT1.

Disease relevance. Retinitis pigmentosa 86 (RP86) [MIM:618613] A form of retinitis pigmentosa, a retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. RP86 is an autosomal recessive form. The disease is caused by variants affecting the gene represented in this entry. A chromosomal aberration involving KIAA1549 is found in pilocytic astrocytoma. A tandem duplication of 2 Mb at 7q34 leads to the expression of a KIAA1549-BRAF fusion protein with a constitutive kinase activity and inducing cell transformation.

Miscellaneous. Produced by alternative promoter usage. Produced by alternative promoter usage.

Similarity. Belongs to the UPF0606 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9HCM3-1	1, v2 long-form	yes
Q9HCM3-2	2, v1 long-form
Q9HCM3-3	3, v1 short-form
Q9HCM3-4	4, v2 short-form

RefSeq proteins (2): NP_001158137, NP_065961 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024606	KIAA1549	Family

Pfam: PF12877

UniProt features (33 total): compositionally biased region 6, modified residue 6, region of interest 6, sequence variant 4, splice variant 3, sequence conflict 3, transmembrane region 2, site 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9HCM3-F1	44.73	0.04

Functional residue map

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

Catalytic / active sites (2): 1643–1644 (breakpoint for translocation to form kiaa1549-braf fusion protein); 1749–1750 (breakpoint for translocation to form kiaa1549-braf fusion protein)

Post-translational modifications (6): 1388, 1395, 1554, 1555, 1622, 1624

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-6802952	Signaling by BRAF and RAF1 fusions
R-HSA-1643685	Disease
R-HSA-5663202	Diseases of signal transduction by growth factor receptors and second messengers
R-HSA-6802957	Oncogenic MAPK signaling

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (5): plasma membrane (GO:0005886), photoreceptor connecting cilium (GO:0032391), cilium (GO:0005929), membrane (GO:0016020), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Oncogenic MAPK signaling	1
Disease	1
Diseases of signal transduction by growth factor receptors and second messengers	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
binding	1
membrane	1
cell periphery	1
ciliary transition zone	1
photoreceptor cell cilium	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

826 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KIAA1549	BRAF	P15056	908
KIAA1549	FAM131B	Q86XD5	796
KIAA1549	NF1	P21359	651
KIAA1549	RNF130	Q86XS8	618
KIAA1549	IDH1	O75874	601
KIAA1549	FGFR1	P11362	588
KIAA1549	SRGAP3	O43295	585
KIAA1549	SRGAP2	O75044	580
KIAA1549	ZFTA	C9JLR9	572
KIAA1549	CLCN6	P51797	554
KIAA1549	MKRN1	Q9UHC7	543
KIAA1549	AKAP9	Q99996	543
KIAA1549	MYBL1	P10243	542
KIAA1549	ATRX	P46100	518
KIAA1549	ARAF	P07557	516

IntAct

47 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
CRTC3	YWHAH	psi-mi:“MI:0914”(association)	0.710
FCN1	POTEF	psi-mi:“MI:0914”(association)	0.530
LGALS1	PODXL	psi-mi:“MI:0914”(association)	0.530
LGALS3	PODXL	psi-mi:“MI:0914”(association)	0.530
SERPINA12	TSPAN6	psi-mi:“MI:0914”(association)	0.530
KIAA1549	CACNA1C	psi-mi:“MI:0915”(physical association)	0.500
OR51E1	KIAA1549	psi-mi:“MI:0915”(physical association)	0.400
OR6A2	KIAA1549	psi-mi:“MI:0915”(physical association)	0.400
SLC5A7	KIAA1549	psi-mi:“MI:0915”(physical association)	0.400
KIAA1549	DST	psi-mi:“MI:0915”(physical association)	0.370
KIAA1549	MYO5B	psi-mi:“MI:0915”(physical association)	0.370
KIAA1549	CADPS	psi-mi:“MI:0915”(physical association)	0.370
KIAA1549	ITSN2	psi-mi:“MI:0915”(physical association)	0.370
KIAA1549	MBD5	psi-mi:“MI:0915”(physical association)	0.370
KIAA1549	Gne	psi-mi:“MI:0915”(physical association)	0.370
KIAA1549		psi-mi:“MI:0915”(physical association)	0.370
M		psi-mi:“MI:0914”(association)	0.350
CACNA1C	SYT5	psi-mi:“MI:0914”(association)	0.350
LGALS8	SLC22A23	psi-mi:“MI:0914”(association)	0.350
ZNF365	RABGAP1L	psi-mi:“MI:0914”(association)	0.350
CEACAM8	PRRT4	psi-mi:“MI:0914”(association)	0.350
LGALS9	PODXL	psi-mi:“MI:0914”(association)	0.350
CXCL6	PPP1R12A	psi-mi:“MI:0914”(association)	0.350
LRRC73	THAP12	psi-mi:“MI:0914”(association)	0.350
PLEKHM3	ENDOD1	psi-mi:“MI:0914”(association)	0.350
OR7A5	UBE4B	psi-mi:“MI:0914”(association)	0.350

BioGRID (105): KIAA1549 (Affinity Capture-MS), KIAA1549 (Affinity Capture-MS), KIAA1549 (Affinity Capture-MS), KIAA1549 (Affinity Capture-MS), KIAA1549 (Affinity Capture-MS), KIAA1549 (Affinity Capture-MS), KIAA1549 (Proximity Label-MS), KIAA1549 (Proximity Label-MS), KIAA1549 (Affinity Capture-MS), KIAA1549 (Affinity Capture-MS), KIAA1549 (Affinity Capture-MS), KIAA1549 (Affinity Capture-MS), KIAA1549 (Affinity Capture-MS), KIAA1549 (Affinity Capture-MS), KIAA1549 (Affinity Capture-RNA)

ESM2 similar proteins: A0JPP4, B7ZCC9, B9EKR1, E9Q7X6, J3KML8, O00592, O57604, P13611, P23471, P30005, P34910, P52549, P70628, Q01036, Q06093, Q1XI86, Q28858, Q2TA21, Q2TBJ9, Q3MIW9, Q3TNW5, Q3TYV2, Q5XI99, Q62059, Q62656, Q62781, Q68FD9, Q69558, Q6MG22, Q6R8J2, Q7TST5, Q80XH2, Q86TY3, Q8BT18, Q8BUE7, Q8C633, Q8IZF6, Q8N3K9, Q8VD58, Q8WXI7

Diamond homologs: Q68FD9, Q6ZVL6, Q9HCM3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

1604 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	4
Uncertain significance	869
Likely benign	574
Benign	68

Top pathogenic / likely-pathogenic (7)

Variant ID	HGVS	Classification
2628030	NM_001164665.2(KIAA1549):c.1827del (p.Ser610fs)	Pathogenic
3064858	NM_001164665.2(KIAA1549):c.2400delinsAA (p.Glu801fs)	Pathogenic
691597	NM_001164665.2(KIAA1549):c.52del (p.Arg18fs)	Pathogenic
1709612	NM_001164665.2(KIAA1549):c.4519C>T (p.Arg1507Ter)	Likely pathogenic
3027921	NM_001164665.2(KIAA1549):c.1796_1797del (p.Glu599fs)	Likely pathogenic
3572940	NM_001164665.2(KIAA1549):c.3823C>T (p.Arg1275Ter)	Likely pathogenic
4280665	NM_001164665.2(KIAA1549):c.4551+1G>C	Likely pathogenic

SpliceAI

3817 predictions. Top by Δscore:

Variant	Effect	Δscore
7:138852217:CCTTA:C	donor_loss	1.0000
7:138852218:CTTA:C	donor_loss	1.0000
7:138852221:A:AC	donor_gain	1.0000
7:138852221:ACCT:A	donor_loss	1.0000
7:138852222:C:CC	donor_gain	1.0000
7:138852265:TATCT:T	acceptor_gain	1.0000
7:138852266:ATCT:A	acceptor_gain	1.0000
7:138852268:CT:C	acceptor_gain	1.0000
7:138852269:TC:T	acceptor_loss	1.0000
7:138852270:C:CC	acceptor_gain	1.0000
7:138852270:CT:C	acceptor_loss	1.0000
7:138852271:T:A	acceptor_loss	1.0000
7:138852278:CA:C	acceptor_gain	1.0000
7:138852279:A:AC	acceptor_gain	1.0000
7:138852279:A:C	acceptor_gain	1.0000
7:138852282:C:CT	acceptor_gain	1.0000
7:138861137:A:AC	donor_gain	1.0000
7:138861138:C:CC	donor_gain	1.0000
7:138861138:CA:C	donor_gain	1.0000
7:138861138:CACT:C	donor_gain	1.0000
7:138861138:CACTG:C	donor_gain	1.0000
7:138861452:TCCGA:T	acceptor_gain	1.0000
7:138861453:CCGA:C	acceptor_gain	1.0000
7:138861453:CCGAC:C	acceptor_gain	1.0000
7:138861454:CGAC:C	acceptor_gain	1.0000
7:138861457:C:CC	acceptor_gain	1.0000
7:138867973:A:AC	donor_gain	1.0000
7:138867974:C:CC	donor_gain	1.0000
7:138868016:T:TA	donor_gain	1.0000
7:138868125:TGAG:T	acceptor_gain	1.0000

AlphaMissense

12569 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:138837967:A:T	I1931N	1.000
7:138869693:C:A	K1540N	1.000
7:138869693:C:G	K1540N	1.000
7:138869697:G:T	A1539D	1.000
7:138869698:C:G	A1539P	1.000
7:138869703:A:G	L1537P	1.000
7:138869706:C:G	R1536P	1.000
7:138869707:G:T	R1536S	1.000
7:138869709:A:G	I1535T	1.000
7:138869711:C:A	K1534N	1.000
7:138869711:C:G	K1534N	1.000
7:138869713:T:C	K1534E	1.000
7:138869714:G:C	N1533K	1.000
7:138869714:G:T	N1533K	1.000
7:138869718:C:G	R1532P	1.000
7:138869719:G:T	R1532S	1.000
7:138869721:T:G	H1531P	1.000
7:138869738:C:A	K1525N	1.000
7:138869738:C:G	K1525N	1.000
7:138869740:T:C	K1525E	1.000
7:138837955:A:G	L1935P	0.999
7:138837964:C:G	R1932P	0.999
7:138837967:A:C	I1931S	0.999
7:138837967:A:G	I1931T	0.999
7:138837971:C:G	A1930P	0.999
7:138837979:A:G	L1927P	0.999
7:138861301:A:C	F1695L	0.999
7:138861301:A:T	F1695L	0.999
7:138861302:A:C	F1695C	0.999
7:138861303:A:G	F1695L	0.999

dbSNP variants (sampled 300 via entrez): RS1000017243 (7:138879124 G>T), RS1000034770 (7:138868984 T>G), RS1000066557 (7:138879376 G>A), RS1000068713 (7:138840433 A>C,T), RS1000093695 (7:138924305 T>G), RS1000097952 (7:138972161 GGCTGGT>G), RS1000126401 (7:138944649 A>C), RS1000160626 (7:138976805 G>T), RS1000170477 (7:138900891 A>G), RS1000184979 (7:138835193 G>C), RS1000198898 (7:138950830 G>A,C), RS1000214996 (7:138956294 A>G), RS1000243298 (7:138939497 A>G), RS1000272163 (7:138913461 A>C,G), RS1000285146 (7:138868518 C>G,T)

Disease associations

OMIM: gene MIM:613344 | disease phenotypes: MIM:618613, MIM:268000

GenCC curated gene-disease

Disease	Classification	Inheritance
retinitis pigmentosa 86	Strong	Autosomal recessive
retinitis pigmentosa	Supportive	Autosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
retinitis pigmentosa 86	Strong	AR

Mondo (4): inherited retinal dystrophy (MONDO:0019118), retinitis pigmentosa 86 (MONDO:0032834), optic atrophy (MONDO:0003608), retinitis pigmentosa (MONDO:0019200)

Orphanet (2): OBSOLETE: Inherited retinal disorder (Orphanet:71862), Retinitis pigmentosa (Orphanet:791)

HPO phenotypes

37 total (30 of 37 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000405	Conductive hearing impairment
HP:0000407	Sensorineural hearing impairment
HP:0000501	Glaucoma
HP:0000505	Visual impairment
HP:0000512	Abnormal electroretinogram
HP:0000529	Progressive visual loss
HP:0000543	Optic disc pallor
HP:0000546	Retinal degeneration
HP:0000551	Color vision defect
HP:0000563	Keratoconus
HP:0000602	Ophthalmoplegia
HP:0000613	Photophobia
HP:0000618	Blindness
HP:0000639	Nystagmus
HP:0000648	Optic atrophy
HP:0000662	Nyctalopia
HP:0000842	Hyperinsulinemia
HP:0001105	Retinal atrophy
HP:0007663	Reduced visual acuity
HP:0007675	Progressive night blindness
HP:0007703	Abnormal retinal pigmentation
HP:0007722	Retinal pigment epithelial atrophy
HP:0007737	Spicular pigmentation of the retina
HP:0007787	Posterior subcapsular cataract
HP:0007843	Attenuation of retinal blood vessels
HP:0007994	Peripheral visual field loss
HP:0008046	Abnormal retinal vascular morphology
HP:0011505	Cystoid macular edema
HP:0012426	Optic disc drusen

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST006979_217	Heel bone mineral density	4.000000e-18

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009270	heel bone mineral density

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
D009896	Optic Atrophy	C10.292.700.225; C11.640.451
D058499	Retinal Dystrophies	C11.768.585.658
D012174	Retinitis Pigmentosa	C11.270.684; C11.768.585.658.500; C16.320.290.684

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Panobinostat	affects cotreatment, decreases expression	2
Estradiol	increases expression	2
Valproic Acid	affects expression, decreases expression	2
dicrotophos	increases expression	1
arsenite	affects binding, decreases reaction	1
potassium chromate(VI)	increases expression	1
perfluorooctane sulfonic acid	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
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Vorinostat	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Folic Acid	decreases expression	1
Methotrexate	increases expression	1
Nickel	decreases expression	1
Phthalic Acids	decreases methylation	1
Sodium Dodecyl Sulfate	increases expression	1
Tetrachlorodibenzodioxin	increases expression	1
Dronabinol	increases expression	1
Tretinoin	decreases expression	1
Urethane	increases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	increases expression	1
Vitamin K 3	affects expression	1
Particulate Matter	increases 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_C7GU	DKFZ-BT308	Cancer cell line	Male
CVCL_C7GW	DKFZ-BT317	Cancer cell line	Male
CVCL_JX58	DKFZ-BT66	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00717080	PHASE4	COMPLETED	The Role of Capsular Tension Ring (CTR) in Anterior Capsular Contraction
NCT00000114	PHASE3	COMPLETED	Randomized Trial of Vitamin A and Vitamin E Supplementation for Retinitis Pigmentosa
NCT00000116	PHASE3	COMPLETED	Randomized Trial of DHA for Retinitis Pigmentosa Patients Receiving Vitamin A
NCT00346333	PHASE3	COMPLETED	Clinical Trial of Lutein for Patients With Retinitis Pigmentosa Receiving Vitamin A
NCT01786395	PHASE3	TERMINATED	Phase III Efficacy and Safety Clinical Study of UF-021 for Treatment of Retinitis Pigmentosa
NCT04224207	PHASE3	COMPLETED	Management of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT04636853	PHASE3	COMPLETED	CB-PRP in Retinitis Pigmentosa and Dry Age-related Macular Degeneration
NCT05537220	PHASE3	ACTIVE_NOT_RECRUITING	Oral N-acetylcysteine for Retinitis Pigmentosa
NCT05800301	PHASE3	COMPLETED	Management of Retinitis Pigmentosa Via Combination of Wharton’s Jelly-derived Mesenchymal Stem Cells and Magnovision
NCT05926583	PHASE3	ACTIVE_NOT_RECRUITING	A Study of AAV5-hRKp.RPGR for the Treatment of Japanese Participants With X-linked Retinitis Pigmentosa
NCT06388200	PHASE3	ACTIVE_NOT_RECRUITING	A Phase 3 Study Of OCU400 Gene Therapy for the Treatment Of Retinitis Pigmentosa
NCT07082855	PHASE3	NOT_YET_RECRUITING	A Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT07290530	PHASE3	NOT_YET_RECRUITING	24-Month Trial of NPI-001 for the Preservation of Photoreceptors in Retinitis Pigmentosa Associated With Usher Syndrome
NCT00100230	PHASE2	COMPLETED	DHA and X-Linked Retinitis Pigmentosa
NCT00447980	PHASE2	COMPLETED	A Study of Encapsulated Cell Technology (ECT) Implant for Participants With Early Stage Retinitis Pigmentosa
NCT00447993	PHASE2	COMPLETED	A Study of Encapsulated Cell Technology (ECT) Implant for Patients With Late Stage Retinitis Pigmentosa
NCT01233609	PHASE2	COMPLETED	Trial of Oral Valproic Acid for Retinitis Pigmentosa
NCT01399515	PHASE2	COMPLETED	Efficacy and Safety of Oral Valproic Acid for Retinitis Pigmentosa
NCT01530659	PHASE2	COMPLETED	Retinal Imaging in CNTF -Releasing Encapsulated Cell Implant Treated Patients for Early-stage Retinitis Pigmentosa
NCT01560715	PHASE2	COMPLETED	Autologous Bone Marrow-Derived Stem Cells Transplantation For Retinitis Pigmentosa
NCT02609165	PHASE2	COMPLETED	Nerve Growth Factor Eye Drops Treatment in Patients With Retinitis Pigmentosa and Cystoid Macular Edema
NCT02661711	PHASE2	COMPLETED	Aflibercept for Macular Oedema With Underlying Retinitis Pigmentosa (AMOUR) Study
NCT02804360	PHASE2	UNKNOWN	Intravitreal Dexamethasone Implant in Retinitis Pigmentosa-related Macular Edema- a Retrospective Study
NCT02837640	PHASE2	UNKNOWN	Studying a Potential Protective Effect of L-Dopa on Retinitis Pigmentosa
NCT03073733	PHASE2	COMPLETED	Safety and Efficacy of Intravitreal Injection of Human Retinal Progenitor Cells in Adults With Retinitis Pigmentosa
NCT04068207	PHASE2	COMPLETED	Minocycline Treatment in Retinitis Pigmentosa
NCT04356716	PHASE2	COMPLETED	Sildenafil for Treatment of Choroidal Ischemia
NCT04604899	PHASE2	COMPLETED	Safety of Repeat Intravitreal Injection of Human Retinal Progenitor Cells (jCell) in Adult Subjects With Retinitis Pigmentosa
NCT04763369	PHASE2	UNKNOWN	Investigation of Therapeutic Efficacy and Safety of UMSCs for the Management of Retinitis Pigmentosa (RP)
NCT04864496	PHASE2	UNKNOWN	Effects of Treatment With N- Acetylcysteine on Visual Outcomes in Patients With Retinitis Pigmentosa
NCT04945772	PHASE2	COMPLETED	Efficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT05085964	PHASE2	TERMINATED	An Open-Label Extension Study to Evaluate Safety & Tolerability of QR-421a in Subjects With Retinitis Pigmentosa
NCT05392179	PHASE2	COMPLETED	A Study in Subjects With Retinitis Pigmentosa
NCT06627179	PHASE2	RECRUITING	Study to Evaluate Ultevursen in Subjects With Retinitis Pigmentosa (RP) Due to Mutations in Exon 13 of the USH2A Gene
NCT06628947	PHASE2	RECRUITING	A Phase II Study of Intravitreal KIO-301 in Patients With Late-stage Retinitis Pigmentosa
NCT06912633	PHASE2	RECRUITING	Safety of a Single, Intravitreal Injection of 6.0M jCell (Famzeretcel) in Retinitis Pigmentosa (RP)
NCT03763227	PHASE2	COMPLETED	Intravitreal Ranibizumab (Lucentis®) in the Treatment of Non-leaking Macular Cysts in Retinal Dystrophy
NCT00063765	PHASE1	COMPLETED	Evaluation of Safety of Ciliary Neurotrophic Factor Implants in the Eye
NCT00065455	PHASE1	COMPLETED	Investigating the Effect of Vitamin A Supplementation on Retinitis Pigmentosa
NCT00458575	PHASE1	TERMINATED	A Study to Evaluate the Safety of CNTO 2476 in Patients With Advanced Retinitis Pigmentosa