SAMD11

Summary

SAMD11 (sterile alpha motif domain containing 11, HGNC:28706) is a protein-coding gene on chromosome 1p36.33, encoding Sterile alpha motif domain-containing protein 11 (Q96NU1). Component of a Polycomb group (PcG) multiprotein PRC1-like complex, essential for establishing rod photoreceptor cell identity and function by silencing nonrod gene expression in developing rod photoreceptor cells.

Predicted to enable several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; identical protein binding activity; and protein domain specific binding activity. Predicted to be involved in negative regulation of DNA-templated transcription and retinal rod cell development. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be part of PRC1 complex. Predicted to be active in nucleus.

Source: NCBI Gene 148398 — RefSeq curated summary.

At a glance

• Gene–disease (curated): retinitis pigmentosa (Strong, GenCC)
• Clinical variants (ClinVar): 1,051 total — 1 pathogenic
• Phenotypes (HPO): 1
• MANE Select transcript: NM_001385641

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28706
Approved symbol	SAMD11
Name	sterile alpha motif domain containing 11
Location	1p36.33
Locus type	gene with protein product
Status	Approved
Aliases	MGC45873
Ensembl gene	ENSG00000187634
Ensembl biotype	protein_coding
OMIM	616765
Entrez	148398

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 14 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000341065, ENST00000342066, ENST00000437963, ENST00000455979, ENST00000464948, ENST00000466827, ENST00000474461, ENST00000478729, ENST00000616016, ENST00000616125, ENST00000617307, ENST00000618181, ENST00000618323, ENST00000618779, ENST00000622503, ENST00000968542, ENST00000968543, ENST00000968544

RefSeq mRNA: 3 — MANE Select: NM_001385641 NM_001385640, NM_001385641, NM_152486

CCDS: CCDS2, CCDS90833, CCDS90834

Canonical transcript exons

ENST00000616016 — 14 exons

Exon	Start	End
ENSE00001637883	923923	924948
ENSE00001708361	939275	939412
ENSE00002692620	943698	943808
ENSE00002728091	942559	943058
ENSE00002733131	943253	943377
ENSE00003477353	941144	941306
ENSE00003675531	942410	942488
ENSE00003794726	925922	926013
ENSE00003845896	943908	944574
ENSE00003911340	935772	935896
ENSE00003911839	931039	931089
ENSE00003912201	939040	939129
ENSE00003913392	942136	942251
ENSE00003915575	930155	930336

Expression profiles

Bgee: expression breadth ubiquitous, 169 present calls, max score 91.22.

FANTOM5 (CAGE): breadth broad, TPM avg 5.8123 / max 106.0223, expressed in 875 samples.

FANTOM5 promoters (13 alternative TSS)

Promoter ID	TPM avg	Samples expressed
24	1.8131	581
26	1.2483	481
27	0.6155	283
36	0.5370	250
33	0.2924	74
28	0.2843	160
39	0.2769	132
38	0.1607	94
37	0.1564	88
25	0.1436	76

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left uterine tube	UBERON:0001303	91.22	gold quality
pituitary gland	UBERON:0000007	90.09	gold quality
adenohypophysis	UBERON:0002196	89.55	gold quality
buccal mucosa cell	CL:0002336	86.24	silver quality
right atrium auricular region	UBERON:0006631	85.47	gold quality
cardiac atrium	UBERON:0002081	84.69	gold quality
spleen	UBERON:0002106	84.36	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.04	gold quality
metanephros cortex	UBERON:0010533	82.06	gold quality
endocervix	UBERON:0000458	79.89	gold quality
prostate gland	UBERON:0002367	79.63	gold quality
descending thoracic aorta	UBERON:0002345	79.43	gold quality
body of uterus	UBERON:0009853	79.40	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.02	gold quality
mucosa of transverse colon	UBERON:0004991	79.02	gold quality
popliteal artery	UBERON:0002250	78.68	gold quality
tibial artery	UBERON:0007610	78.66	gold quality
left adrenal gland cortex	UBERON:0035825	78.57	gold quality
right adrenal gland	UBERON:0001233	78.44	gold quality
lower esophagus	UBERON:0013473	77.93	gold quality
lower esophagus muscularis layer	UBERON:0035833	77.92	gold quality
left adrenal gland	UBERON:0001234	77.79	gold quality
right uterine tube	UBERON:0001302	77.72	gold quality
aorta	UBERON:0000947	77.52	gold quality
mucosa of stomach	UBERON:0001199	77.48	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	77.44	gold quality
stromal cell of endometrium	CL:0002255	77.17	gold quality
right adrenal gland cortex	UBERON:0035827	76.93	gold quality
adult mammalian kidney	UBERON:0000082	76.67	gold quality
adrenal cortex	UBERON:0001235	76.61	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-31	yes	468.66
E-MTAB-5061	yes	234.12
E-ENAD-27	yes	92.43
E-GEOD-83139	yes	77.09
E-GEOD-81608	yes	22.92
E-ANND-3	yes	3.51

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting SAMD11, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-19A-5P	99.36	66.93	1675
HSA-MIR-19B-1-5P	99.36	67.07	1669
HSA-MIR-19B-2-5P	99.36	67.07	1669
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-4758-3P	99.12	63.96	869
HSA-MIR-4254	99.11	65.15	1315
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-4656	98.79	66.22	1306
HSA-MIR-4725-5P	98.67	65.42	628
HSA-MIR-504-5P	98.67	65.40	631
HSA-MIR-4675	97.69	64.82	774
HSA-MIR-4741	97.69	64.14	883
HSA-MIR-3620-5P	97.42	63.95	792
HSA-MIR-6736-3P	96.98	65.22	1342
HSA-MIR-1587	96.95	64.03	932
HSA-MIR-3918	96.13	64.65	1300

Literature-anchored findings (GeneRIF, showing 4)

• SAMD11 was found to be widely expressed in many cell lines and ocular tissues and its transcription was not regulated by CRX, OTX2 or NR2E3 proteins. (PMID:23978614)
• SEZ6L, HISPPD1, FEZF1, SAMD11 gene variants may be associated with autism spectrum disorder. (PMID:26204995)
• analysis of a homozygous nonsense mutation in SAMD11 in five individuals diagnosed with adult-onset retinitis pigmentosa; SAMD11 interacts with CRX and is expressed in retina (PMID:27734943)
• CircSAMD11 facilitates progression of cervical cancer via regulating miR-503/SOX4 axis through Wnt/beta-catenin pathway. (PMID:34546569)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	samd11	ENSDARG00000077852
mus_musculus	Samd11	ENSMUSG00000096351
rattus_norvegicus	Samd11	ENSRNOG00000020342
drosophila_melanogaster	l(3)mbt	FBGN0002441
drosophila_melanogaster	Sfmbt	FBGN0032475
caenorhabditis_elegans	lin-61	WBGENE00003041
caenorhabditis_elegans	mbtr-1	WBGENE00021661

Paralogs (18): SCMH1 (ENSG00000010803), MBTD1 (ENSG00000011258), SCML1 (ENSG00000047634), L3MBTL2 (ENSG00000100395), SCML2 (ENSG00000102098), PHC1 (ENSG00000111752), THAP10 (ENSG00000129028), PHC2 (ENSG00000134686), SAMD1 (ENSG00000141858), SCML4 (ENSG00000146285), L3MBTL4 (ENSG00000154655), SFMBT1 (ENSG00000163935), PHC3 (ENSG00000173889), L3MBTL1 (ENSG00000185513), SAMD7 (ENSG00000187033), SFMBT2 (ENSG00000198879), L3MBTL3 (ENSG00000198945), SAMD13 (ENSG00000203943)

Protein

Protein identifiers

Sterile alpha motif domain-containing protein 11 — Q96NU1 (reviewed: Q96NU1)

All UniProt accessions (11): A0A087WU74, A0A087WX24, A0A087WXB3, A0A087WYU3, A0A087WYW1, A0A087X1J5, A0A087X223, Q96NU1, H7BY14, H7C3J6, Q5SV95

UniProt curated annotations — full annotation on UniProt →

Function. Component of a Polycomb group (PcG) multiprotein PRC1-like complex, essential for establishing rod photoreceptor cell identity and function by silencing nonrod gene expression in developing rod photoreceptor cells.

Subunit / interactions. Self-associates. Component of a Polycomb group (PcG) multiprotein PRC1-like complex. Interacts with SAMD7 and PHC2.

Subcellular location. Nucleus.

Tissue specificity. Expressed in the outer and inner nuclear layers, ganglion cell layer and rod photoreceptors of the retina (at protein level). Widely expressed, showing the highest expression in kidney, prostate and retina.

Disease relevance. Retinitis pigmentosa (RP) [MIM:268000] 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. Retinitis pigmentosa can be inherited as an autosomal dominant, autosomal recessive or X-linked condition. Disease susceptibility may be associated with variants affecting the gene represented in this entry.

Miscellaneous. Produced by alternative promoter usage. Produced by alternative promoter usage and alternative splicing. Produced by alternative splicing. Produced by alternative splicing. Produced by alternative splicing.

Isoforms (6)

UniProt ID	Names	Canonical?
Q96NU1-3	3, FL-SAMD11	yes
Q96NU1-1	1, SAMD11-ASV
Q96NU1-2	2, AP-SAMD11-ASV
Q96NU1-4	4, SAMD11-ASV5
Q96NU1-5	5, SAMD11-ASV1
Q96NU1-6	6, SAMD11-ASV6

RefSeq proteins (3): NP_001372569, NP_001372570, NP_689699 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001660	SAM	Domain
IPR013761	SAM/pointed_sf	Homologous_superfamily

Pfam: PF07647

UniProt features (24 total): region of interest 5, compositionally biased region 4, splice variant 4, sequence variant 3, sequence conflict 3, modified residue 2, chain 1, domain 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96NU1-F1	50.57	0.09

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 (3): 485, 640, 72

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 123 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, BENPORATH_ES_WITH_H3K27ME3, GOBP_NEUROGENESIS, HNF1_Q6, GOBP_NEURAL_RETINA_DEVELOPMENT, NKX61_01, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_EYE_PHOTORECEPTOR_CELL_DIFFERENTIATION, GOBP_PHOTORECEPTOR_CELL_DEVELOPMENT, GOBP_CAMERA_TYPE_EYE_PHOTORECEPTOR_CELL_DIFFERENTIATION, GATA1_04, GOBP_PHOTORECEPTOR_CELL_DIFFERENTIATION, GOCC_NUCLEAR_UBIQUITIN_LIGASE_COMPLEX, POU3F2_02, GOBP_SENSORY_ORGAN_DEVELOPMENT

GO Biological Process (3): negative regulation of DNA-templated transcription (GO:0045892), retinal rod cell development (GO:0046548), negative regulation of transcription by RNA polymerase II (GO:0000122)

GO Molecular Function (6): DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), chromatin binding (GO:0003682), histone binding (GO:0042393), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), PRC1 complex (GO:0035102)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
DNA-templated transcription	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
eye photoreceptor cell development	1
retinal rod cell differentiation	1
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
negative regulation of transcription by RNA polymerase II	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription repressor activity	1
protein binding	1
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear ubiquitin ligase complex	1
PcG protein complex	1

Protein interactions and networks

STRING

492 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SAMD11	KLHL17	Q6TDP4	511
SAMD11	NR2E3	Q9Y5X4	404
SAMD11	ZNF408	Q9H9D4	397
SAMD11	PUSL1	Q8N0Z8	376
SAMD11	OR4F17	Q8NGA8	373
SAMD11	OR4F5	Q8NH21	370
SAMD11	Q3MI93	Q3MI93	370
SAMD11	ZNF276	Q8N554	350
SAMD11	SPINDOC	Q9BUA3	349
SAMD11	VWA1	Q6PCB0	349
SAMD11	CCDC154	A6NI56	348
SAMD11	VPS9D1	Q9Y2B5	342
SAMD11	SPOCD1	Q6ZMY3	336
SAMD11	A1CF	Q9NQ94	327
SAMD11	CRX	O43186	325

IntAct

76 interactions, top by confidence:

A	B	Type	Score
YWHAG	BLTP3B	psi-mi:“MI:0914”(association)	0.640
YWHAE	PIK3C2A	psi-mi:“MI:0914”(association)	0.570
YWHAH	BLTP3B	psi-mi:“MI:0914”(association)	0.570
SAMD11	CT55	psi-mi:“MI:0915”(physical association)	0.560
KRT31	SAMD11	psi-mi:“MI:0915”(physical association)	0.560
REL	SAMD11	psi-mi:“MI:0915”(physical association)	0.560
PRR20D	SAMD11	psi-mi:“MI:0915”(physical association)	0.560
TRAF1	SAMD11	psi-mi:“MI:0915”(physical association)	0.560
KRTAP5-7	SAMD11	psi-mi:“MI:0915”(physical association)	0.560
TRAF2	SAMD11	psi-mi:“MI:0915”(physical association)	0.560
KRT34	SAMD11	psi-mi:“MI:0915”(physical association)	0.560
SAMD11	PLAGL2	psi-mi:“MI:0915”(physical association)	0.560
JMJD7	SAMD11	psi-mi:“MI:0915”(physical association)	0.560
ECM1	SAMD11	psi-mi:“MI:0915”(physical association)	0.560
RTL8C	SAMD11	psi-mi:“MI:0915”(physical association)	0.560
SAMD11	PLEKHF2	psi-mi:“MI:0915”(physical association)	0.560
TSC1	SAMD11	psi-mi:“MI:0915”(physical association)	0.560
CT55	SAMD11	psi-mi:“MI:0915”(physical association)	0.560
NFKBID	SAMD11	psi-mi:“MI:0915”(physical association)	0.560
SAMD11	TRIB3	psi-mi:“MI:0915”(physical association)	0.560
SAMD11	BPIFA1	psi-mi:“MI:0915”(physical association)	0.560
CCHCR1	SAMD11	psi-mi:“MI:0915”(physical association)	0.560
SAMD11	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
SAMD7	GAPDHS	psi-mi:“MI:0914”(association)	0.530
PRR20E	SIAH2	psi-mi:“MI:0914”(association)	0.530
YES1	SAMD11	psi-mi:“MI:0407”(direct interaction)	0.440
SAMD11		psi-mi:“MI:0915”(physical association)	0.370
KLF15		psi-mi:“MI:0914”(association)	0.350
KLF8		psi-mi:“MI:0914”(association)	0.350

BioGRID (52): SAMD11 (Affinity Capture-MS), SAMD11 (Affinity Capture-MS), SAMD11 (Affinity Capture-MS), SAMD11 (Affinity Capture-MS), SAMD11 (Affinity Capture-MS), SAMD11 (Affinity Capture-MS), SAMD11 (Affinity Capture-MS), SAMD11 (Affinity Capture-MS), SAMD11 (Affinity Capture-RNA), SAMD11 (Two-hybrid), SAMD11 (Two-hybrid), SAMD11 (Two-hybrid), SAMD11 (Two-hybrid), SAMD11 (Two-hybrid), SAMD11 (Two-hybrid)

ESM2 similar proteins: A2A699, A2A7S8, A2AEV7, A5PKW4, A8MVW0, F1MUS9, O14559, O15049, O88881, O95886, P60669, P97838, Q03484, Q3B8N7, Q3KP66, Q3LUD3, Q3LUD4, Q5BJT1, Q5DTT2, Q5ZLT3, Q63HR2, Q66H43, Q68EF6, Q69YU3, Q6PDH0, Q6PFD5, Q6R6L0, Q6ZVC0, Q7TN12, Q80VC9, Q86UU1, Q86WR7, Q8C7U1, Q8CGB6, Q8VC98, Q8WUF5, Q924A2, Q96EL1, Q96FS4, Q96HB5

Diamond homologs: A2A5N8, B1B1A0, D3YUG0, D3YXK1, D3ZWK4, E1C2V1, O02274, O60284, O95251, P39769, P59178, P70047, P70475, P78364, P97500, Q01538, Q05BQ5, Q1JQD9, Q1RNF8, Q29L50, Q32N90, Q3MIF2, Q4V7W5, Q5DTW2, Q5R737, Q5SVQ0, Q5VUG0, Q5VXD3, Q64028, Q6DIN3, Q6P5G3, Q6SPE9, Q6SPF0, Q7Z3H4, Q80TY4, Q810T5, Q8BLB7, Q8C8Y5, Q8CFC2, Q8CHP6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 48 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
TP53 Regulates Metabolic Genes	5	20.9×	8e-05
Transcriptional Regulation by TP53	5	10.0×	1e-03
Signaling by Rho GTPases	6	6.6×	2e-03
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	6	6.5×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

1051 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	531
Likely benign	438
Benign	59

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
950448	NM_001385641.1(SAMD11):c.2377C>T (p.Arg793Ter)	Pathogenic

SpliceAI

2561 predictions. Top by Δscore:

Variant	Effect	Δscore
1:939130:G:GA	donor_loss	1.0000
1:939131:T:G	donor_loss	1.0000
1:939271:GCA:G	acceptor_gain	1.0000
1:939271:GCAGA:G	acceptor_gain	1.0000
1:942471:G:GT	donor_gain	1.0000
1:943365:A:T	donor_gain	1.0000
1:943696:A:AG	acceptor_gain	1.0000
1:943696:AG:A	acceptor_gain	1.0000
1:943697:G:GT	acceptor_gain	1.0000
1:943697:GG:G	acceptor_gain	1.0000
1:943697:GGT:G	acceptor_gain	1.0000
1:943697:GGTC:G	acceptor_gain	1.0000
1:943697:GGTCT:G	acceptor_gain	1.0000
1:943804:CCCAG:C	donor_loss	1.0000
1:943806:CAGG:C	donor_loss	1.0000
1:943807:AGG:A	donor_loss	1.0000
1:943808:GG:G	donor_loss	1.0000
1:943810:T:G	donor_loss	1.0000
1:930144:T:TA	acceptor_gain	0.9900
1:930151:CCAGA:C	acceptor_loss	0.9900
1:930152:CA:C	acceptor_loss	0.9900
1:930153:A:AC	acceptor_loss	0.9900
1:930153:A:AG	acceptor_gain	0.9900
1:930154:G:GG	acceptor_gain	0.9900
1:930154:GA:G	acceptor_gain	0.9900
1:930302:G:GT	donor_gain	0.9900
1:930332:AGAAG:A	donor_loss	0.9900
1:930334:AAGG:A	donor_loss	0.9900
1:930335:AGGTA:A	donor_loss	0.9900
1:930336:GGT:G	donor_loss	0.9900

AlphaMissense

5712 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:943756:T:C	L583P	0.999
1:925993:T:C	C18R	0.998
1:943315:T:A	W543R	0.998
1:943315:T:C	W543R	0.998
1:943331:T:A	V548D	0.998
1:943702:T:C	F565S	0.998
1:943741:T:C	L578P	0.998
1:943789:C:A	A594D	0.998
1:943798:T:C	I597T	0.998
1:925979:G:A	C13Y	0.997
1:925984:T:C	C15R	0.997
1:925993:T:A	C18S	0.997
1:925994:G:C	C18S	0.997
1:943317:G:C	W543C	0.997
1:943317:G:T	W543C	0.997
1:943717:T:A	I570N	0.997
1:943774:T:C	L589P	0.997
1:943792:T:C	L595P	0.997
1:943798:T:G	I597S	0.997
1:925978:T:C	C13R	0.996
1:926000:T:C	I20T	0.996
1:943339:T:C	F551L	0.996
1:943340:T:C	F551S	0.996
1:943341:C:A	F551L	0.996
1:943341:C:G	F551L	0.996
1:943701:T:C	F565L	0.996
1:943702:T:G	F565C	0.996
1:943703:C:A	F565L	0.996
1:943703:C:G	F565L	0.996
1:943722:G:T	G572W	0.996

dbSNP variants (sampled 300 via entrez): RS1000001574 (1:926128 G>A), RS1000034279 (1:923187 T>C), RS1000217911 (1:940252 G>GCGCCGGC), RS1000271567 (1:940341 G>GT), RS1000276322 (1:933315 G>A,T), RS1000287307 (1:936770 C>G,T), RS1000407280 (1:936871 ATGAT>A), RS1000413267 (1:939606 G>A,T), RS1000470702 (1:922016 C>T), RS1000586496 (1:922254 A>C,T), RS1000610952 (1:939592 C>A,T), RS1000750610 (1:942424 C>T), RS1000823443 (1:943592 T>G), RS1000874657 (1:944746 G>A,C), RS1000889684 (1:940702 C>G,T)

Disease associations

OMIM: gene MIM:616765 | disease phenotypes: MIM:268000

GenCC curated gene-disease

Disease	Classification	Inheritance
retinitis pigmentosa	Strong	Autosomal recessive

Mondo (3): inherited retinal dystrophy (MONDO:0019118), optic atrophy (MONDO:0003608), retinitis pigmentosa (MONDO:0019200)

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

HPO phenotypes

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

HPO	Term
HP:0000556	Retinal dystrophy

GWAS associations

0 associations (top):

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

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, increases expression, affects methylation, affects cotreatment	3
Estradiol	affects expression, affects cotreatment, increases expression, decreases expression	3
Tretinoin	increases expression, decreases expression	2
Valproic Acid	affects expression, increases methylation	2
aristolochic acid I	decreases expression	1
bisphenol F	affects cotreatment, increases methylation	1
TAK-243	increases sumoylation	1
bisphenol A	affects cotreatment, increases methylation, decreases methylation	1
2,5,2’,5’-tetrachlorobiphenyl	increases expression	1
sulforaphane	decreases expression	1
butyraldehyde	decreases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
ferrous chloride	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
abrine	decreases expression	1
ormosil	affects binding, decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	decreases methylation	1
jinfukang	affects cotreatment, decreases expression	1
Zoledronic Acid	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Vorinostat	affects cotreatment, increases expression	1
Leflunomide	increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	affects cotreatment, decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1

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