FAM161A

Summary

FAM161A (FAM161 centrosomal protein A, HGNC:25808) is a protein-coding gene on chromosome 2p15, encoding Protein FAM161A (Q3B820). Involved in ciliogenesis.

This gene belongs to the FAM161 family. It is expressed mainly in the retina. Mouse studies suggested that this gene is involved in development of retinal progenitors during embryogenesis, and that its activity is restricted to mature photoreceptors after birth. Mutations in this gene cause autosomal recessive retinitis pigmentosa-28. Alternatively spliced transcript variants have been identified.

Source: NCBI Gene 84140 — RefSeq curated summary.

At a glance

• Gene–disease (curated): retinitis pigmentosa 28 (Definitive, GenCC) — +1 more curated relationship
• GWAS associations: 4
• Clinical variants (ClinVar): 959 total — 95 pathogenic, 63 likely-pathogenic
• Phenotypes (HPO): 34
• Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
• MANE Select transcript: NM_001201543

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25808
Approved symbol	FAM161A
Name	FAM161 centrosomal protein A
Location	2p15
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13305
Ensembl gene	ENSG00000170264
Ensembl biotype	protein_coding
OMIM	613596
Entrez	84140

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 3 nonsense_mediated_decay, 3 protein_coding, 2 retained_intron

ENST00000307507, ENST00000404929, ENST00000405894, ENST00000418113, ENST00000456262, ENST00000478494, ENST00000496369, ENST00000915467

RefSeq mRNA: 2 — MANE Select: NM_001201543 NM_001201543, NM_032180

CCDS: CCDS42687, CCDS56120

Canonical transcript exons

ENST00000404929 — 7 exons

Exon	Start	End
ENSE00001550672	61853859	61854060
ENSE00001554103	61838538	61838705
ENSE00003489321	61836010	61836109
ENSE00003541204	61827104	61827258
ENSE00003613756	61842122	61842360
ENSE00003650570	61839421	61840581
ENSE00003842678	61824848	61826599

Expression profiles

Bgee: expression breadth ubiquitous, 215 present calls, max score 95.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.3524 / max 88.0730, expressed in 1152 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
28676	3.5452	1079
28675	0.4354	244
28678	0.2316	103
28677	0.0736	35
28674	0.0665	25

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pigmented layer of retina	UBERON:0001782	95.29	gold quality
retina	UBERON:0000966	95.27	gold quality
sperm	CL:0000019	92.06	gold quality
secondary oocyte	CL:0000655	90.00	gold quality
bronchial epithelial cell	CL:0002328	88.34	gold quality
epithelium of bronchus	UBERON:0002031	88.00	gold quality
oviduct epithelium	UBERON:0004804	87.59	gold quality
bronchus	UBERON:0002185	86.67	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.10	gold quality
cortical plate	UBERON:0005343	85.76	gold quality
ventricular zone	UBERON:0003053	85.47	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.32	gold quality
embryo	UBERON:0000922	84.27	gold quality
ganglionic eminence	UBERON:0004023	84.27	gold quality
right testis	UBERON:0004534	84.26	gold quality
testis	UBERON:0000473	84.06	gold quality
left testis	UBERON:0004533	84.05	gold quality
right uterine tube	UBERON:0001302	82.76	gold quality
fallopian tube	UBERON:0003889	78.53	gold quality
left ovary	UBERON:0002119	78.11	gold quality
body of pancreas	UBERON:0001150	78.03	gold quality
ovary	UBERON:0000992	77.86	gold quality
right ovary	UBERON:0002118	77.50	gold quality
oocyte	CL:0000023	77.24	gold quality
mucosa of paranasal sinus	UBERON:0005030	77.11	gold quality
pituitary gland	UBERON:0000007	76.88	gold quality
body of stomach	UBERON:0001161	76.50	gold quality
adenohypophysis	UBERON:0002196	76.29	gold quality
Brodmann (1909) area 23	UBERON:0013554	75.38	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	75.25	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	44.04
E-GEOD-137537	yes	19.62
E-ANND-3	yes	5.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

105 targeting FAM161A, 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-6758-5P	100.00	66.21	1470
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 16)

• Null mutations in FAM161A are responsible for the RP28-associated autosomal-recessive retinitis pigmentosa. (PMID:20705278)
• These data suggest a pivotal role for FAM161A in photoreceptors and reveal that FAM161A loss-of-function mutations are a major cause of autosomal-recessive Retinitis pigmentosa. (PMID:20705279)
• FAM161A is a microtubule-associated ciliary protein presumably involved in microtubule stabilization to maintain the microtubule tracks and/or in transport processes along microtubules in photoreceptors and other retinal cell types. (PMID:22791751)
• FAM161A-associated RP can be considered as a novel retinal ciliopathy and that its molecular pathogenesis may be related to other ciliopathies. (PMID:22940612)
• an RP28 (an autosomal recessive form of retinitis pigmentosa)-linked RP family in the Palestinian population caused by a novel nonsense mutation in FAM161A, was identified. (PMID:24520187)
• Our data indicate that mutations in FAM161A are responsible for 1% of recessive RP cases in North America, similar to the prevalence detected in Germany and unlike the data from Israel and the Palestinian territories. (PMID:24651477)
• FAM161A is a novel centrosomal-ciliary protein that likely is implicated in the regulation of microtubule-based cellular processes in the retina. (PMID:24664697)
• Exome analysis revealed a nonsense homozygous mutation in FAM161A segregating with retinal degeneration with severe vision loss and a range of disease onset and progression. (PMID:25007332)
• Yeast two-hybrid screening of a human retinal cDNA library revealed FAM161A as a binary interaction partner of POC1B. (PMID:25018096)
• FAM161A’s activities are probably not limited to ciliary tasks but also extend to more general cellular functions, highlighting possible novel mechanisms for the molecular pathology of retinal disease. (PMID:25749990)
• We screened a panel of 120 probands with recessive Retinitis Pigmentosa, and two were found to harbour biallelic FAM161A variants. (PMID:26113502)
• novel homozygous frameshift mutations of RP28-linked RP gene FAM161A in Indian population. (PMID:26246154)
• founder mutation in FAM161A p.(Arg437*) underlies approximately 2% of arRP cases in the Dutch and Belgian populations. (PMID:26574802)
• Unique combination of clinical features in a large cohort of 100 patients with retinitis pigmentosa caused by FAM161A mutations. (PMID:32938956)
• Structural bioinformatics predicts that the Retinitis Pigmentosa-28 protein of unknown function FAM161A is a homologue of the microtubule nucleation factor Tpx2. (PMID:33093951)
• Interactions between C8orf37 and FAM161A, Two Ciliary Proteins Essential for Photoreceptor Survival. (PMID:36233334)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam161a	ENSDARG00000089742
mus_musculus	Fam161a	ENSMUSG00000049811
rattus_norvegicus	Fam161a	ENSRNOG00000009881

Paralogs (2): FAM161B (ENSG00000156050), TSGA10IP (ENSG00000175513)

Protein

Protein identifiers

Protein FAM161A — Q3B820 (reviewed: Q3B820)

All UniProt accessions (4): Q3B820, F8W731, F8WCZ8, H7C4C9

UniProt curated annotations — full annotation on UniProt →

Function. Involved in ciliogenesis.

Subunit / interactions. Interacts (via central region) with CFAP418 (via N-terminus); the interaction is direct. Interacts (via C-terminus) with microtubules. Interacts with LCA5. Interacts with CEP290. Interacts with SDCCAG8. Interacts with FAM161B. Interacts with POC1B. Interacts with CEP78. Forms a microtubule-associated complex with POC5, CETN2 and POC1B. Interacts with CCDC15.

Subcellular location. Cytoplasm. Cytoskeleton. Cilium basal body. Cell projection. Cilium. Microtubule organizing center. Centrosome. Centriole.

Tissue specificity. Isoform 1 and isoform 3 are widely expressed with highest levels in retina and testis, with isoform 1 being the most abundant in all tissues tested.

Disease relevance. Retinitis pigmentosa 28 (RP28) [MIM:606068] 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. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the FAM161 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q3B820-1	1	yes
Q3B820-2	2
Q3B820-3	3

RefSeq proteins (2): NP_001188472, NP_115556 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019579	FAM161A/B	Family
IPR051655	FAM161	Family

Pfam: PF10595

UniProt features (19 total): sequence variant 4, sequence conflict 3, coiled-coil region 3, region of interest 2, splice variant 2, compositionally biased region 2, cross-link 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3B820-F1	66.83	0.17

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 (2): 468, 484

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 180 (showing top): GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, GOBP_CILIUM_ORGANIZATION, GOCC_CENTROSOME, GOBP_ORGANELLE_ASSEMBLY, GOBP_SENSORY_PERCEPTION, FISCHER_DREAM_TARGETS, GOCC_NEURON_PROJECTION, GOBP_CELL_PROJECTION_ORGANIZATION, CHANG_IMMORTALIZED_BY_HPV31_UP, VERNELL_RETINOBLASTOMA_PATHWAY_UP, GOCC_SPINDLE, GOCC_CENTRIOLE, GOCC_MITOTIC_SPINDLE, BROWNE_HCMV_INFECTION_14HR_UP

GO Biological Process (4): visual perception (GO:0007601), cilium organization (GO:0044782), cilium assembly (GO:0060271), cell projection organization (GO:0030030)

GO Molecular Function (3): microtubule binding (GO:0008017), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (16): astral microtubule (GO:0000235), photoreceptor inner segment (GO:0001917), nucleoplasm (GO:0005654), Golgi apparatus (GO:0005794), centrosome (GO:0005813), centriole (GO:0005814), cytosol (GO:0005829), spindle microtubule (GO:0005876), photoreceptor connecting cilium (GO:0032391), ciliary basal body (GO:0036064), mitotic spindle (GO:0072686), mitotic spindle pole (GO:0097431), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
microtubule organizing center	3
cytoplasm	2
intracellular membraneless organelle	2
spindle	2
sensory perception of light stimulus	1
organelle organization	1
plasma membrane bounded cell projection organization	1
axoneme assembly	1
intraciliary transport involved in cilium assembly	1
cilium organization	1
protein localization to cilium	1
organelle assembly	1
trans-Golgi to periciliary membrane compartment transport	1
plasma membrane bounded cell projection assembly	1
ciliary transition zone assembly	1
cellular component organization	1
tubulin binding	1
protein binding	1
binding	1
aster	1
spindle microtubule	1
cytoplasmic microtubule	1
nuclear lumen	1
endomembrane system	1
intracellular membrane-bounded organelle	1
centriole	1
microtubule	1
ciliary transition zone	1
photoreceptor cell cilium	1
cilium	1
spindle pole	1
mitotic spindle	1
intracellular anatomical structure	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

2619 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM161A	POC1B	Q8TC44	935
FAM161A	POC5	Q8NA72	913
FAM161A	CRX	O43186	797
FAM161A	PDE6B	P35913	788
FAM161A	LCA5	Q86VQ0	741
FAM161A	WDR90	Q96KV7	708
FAM161A	DHDDS	Q86SQ9	695
FAM161A	CERKL	Q49MI3	692
FAM161A	EYS	Q5T1H1	676
FAM161A	RHO	P08100	652
FAM161A	PCARE	A6NGG8	645
FAM161A	SPATA7	Q9P0W8	624
FAM161A	RPGR	Q92834	613
FAM161A	USH2A	O75445	609
FAM161A	ZNF513	Q8N8E2	601

IntAct

547 interactions, top by confidence:

A	B	Type	Score
FAM161A	DHX32	psi-mi:“MI:0915”(physical association)	0.840
FAM161A	TFIP11	psi-mi:“MI:0915”(physical association)	0.840
DHX32	FAM161A	psi-mi:“MI:0915”(physical association)	0.840
TFIP11	FAM161A	psi-mi:“MI:0915”(physical association)	0.840
POC5	FAM161A	psi-mi:“MI:0915”(physical association)	0.800
FAM161A	POC5	psi-mi:“MI:0915”(physical association)	0.800
FAM161A	PNMA2	psi-mi:“MI:0915”(physical association)	0.740
CCDC102B	FAM161A	psi-mi:“MI:0915”(physical association)	0.720
CADPS	FAM161A	psi-mi:“MI:0915”(physical association)	0.720
FAM161A	KRTAP5-9	psi-mi:“MI:0915”(physical association)	0.720
FAM161A	CDR2	psi-mi:“MI:0915”(physical association)	0.720
CALCOCO2	FAM161A	psi-mi:“MI:0915”(physical association)	0.720
TNIP1	FAM161A	psi-mi:“MI:0915”(physical association)	0.720
HMBOX1	FAM161A	psi-mi:“MI:0915”(physical association)	0.720
CEP70	FAM161A	psi-mi:“MI:0915”(physical association)	0.720
FAM161A	MIPOL1	psi-mi:“MI:0915”(physical association)	0.720
ZBTB8A	FAM161A	psi-mi:“MI:0915”(physical association)	0.720
MDFI	FAM161A	psi-mi:“MI:0915”(physical association)	0.720
FAM161A	LZTS2	psi-mi:“MI:0915”(physical association)	0.720
TRIM54	FAM161A	psi-mi:“MI:0915”(physical association)	0.720
MID2	FAM161A	psi-mi:“MI:0915”(physical association)	0.720
ZBTB1	FAM161A	psi-mi:“MI:0915”(physical association)	0.720
FAM161A	CCDC102B	psi-mi:“MI:0915”(physical association)	0.720
FAM161A	CADPS	psi-mi:“MI:0915”(physical association)	0.720
KRTAP5-9	FAM161A	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (204): FAM161A (Two-hybrid), FAM161A (Two-hybrid), FAM161A (Two-hybrid), FAM161A (Two-hybrid), FAM161A (Two-hybrid), FAM161A (Two-hybrid), FAM161A (Two-hybrid), FAM161A (Two-hybrid), FAM161A (Two-hybrid), FAM161A (Two-hybrid), FAM161A (Two-hybrid), FAM161A (Two-hybrid), FAM161A (Two-hybrid), FAM161A (Two-hybrid), FAM161A (Two-hybrid)

ESM2 similar proteins: A0A1B0GTD5, A0A1B0GUX0, A0A3Q1LFK7, A0A3Q1MT14, A2BFC9, A4II40, A4QMS7, A6NJV1, A6NL82, A8QW39, B0BM24, B0UXH9, B5X5D0, B9EJX3, E1B9R1, E1BNS6, F1MMV1, F1P3Y5, H3BRN8, Q0VB26, Q2T9Q3, Q2TA11, Q32L72, Q32P67, Q3B820, Q3SZR5, Q4KKZ1, Q5BN45, Q5BN46, Q5M7D8, Q5M7F8, Q5NC57, Q5SPV6, Q5SVJ3, Q5VZQ5, Q6AYM0, Q6P3G4, Q6ZVS7, Q8CDT5, Q8CDU5

Diamond homologs: A5D7I0, Q3B820, Q3SY00, Q66MI6, Q8CB59, B0BM24, Q66KE9, Q6AY14, Q8QZV6, Q96MY7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 68 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.

GO biological processes:

GO term	Partners	Fold	FDR
cilium assembly	6	8.2×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	95
Likely pathogenic	63
Uncertain significance	355
Likely benign	347
Benign	18

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1069448	NM_001201543.2(FAM161A):c.406_407del (p.Ser135_Leu136insTer)	Pathogenic
1069767	NM_001201543.2(FAM161A):c.1534_1538del (p.Asn512fs)	Pathogenic
1070699	NM_001201543.2(FAM161A):c.1448del (p.Asn482_Leu483insTer)	Pathogenic
1070713	NM_001201543.2(FAM161A):c.1842del (p.Val615fs)	Pathogenic
1071825	NM_001201543.2(FAM161A):c.1157dup (p.Arg387fs)	Pathogenic
1072059	NM_001201543.2(FAM161A):c.1535_1547del (p.Asn512fs)	Pathogenic
1074057	NM_001201543.2(FAM161A):c.1570G>T (p.Glu524Ter)	Pathogenic
1074861	NM_001201543.2(FAM161A):c.1388del (p.Pro463fs)	Pathogenic
1075311	NM_001201543.2(FAM161A):c.1750A>T (p.Arg584Ter)	Pathogenic
1075464	NM_001201543.2(FAM161A):c.549del (p.Glu184fs)	Pathogenic
1075585	NM_001201543.2(FAM161A):c.1720C>T (p.Gln574Ter)	Pathogenic
1213998	NM_001201543.2(FAM161A):c.1095T>G (p.Tyr365Ter)	Pathogenic
1365898	NM_001201543.2(FAM161A):c.945dup (p.Glu316fs)	Pathogenic
1397312	NM_001201543.2(FAM161A):c.964C>T (p.Gln322Ter)	Pathogenic
1404914	NM_001201543.2(FAM161A):c.1759G>T (p.Glu587Ter)	Pathogenic
1409472	NC_000002.11:g.(?62051973)(62063254_?)del	Pathogenic
1424002	NM_001201543.2(FAM161A):c.1777G>T (p.Glu593Ter)	Pathogenic
1425683	NM_001201543.2(FAM161A):c.119del (p.Ala40fs)	Pathogenic
1432298	NM_001201543.2(FAM161A):c.876del (p.Leu293fs)	Pathogenic
1438349	NM_001201543.2(FAM161A):c.1804G>T (p.Glu602Ter)	Pathogenic
1443320	NM_001201543.2(FAM161A):c.1356_1357del (p.Val453_Cys454insTer)	Pathogenic
1445822	NM_001201543.2(FAM161A):c.13del (p.His5fs)	Pathogenic
1451752	NM_001201543.2(FAM161A):c.754A>T (p.Lys252Ter)	Pathogenic
1452178	NM_001201543.2(FAM161A):c.1839_1842del (p.Arg614fs)	Pathogenic
1452779	NM_001201543.2(FAM161A):c.608G>A (p.Trp203Ter)	Pathogenic
1452882	NC_000002.11:g.(?62080984)(62081288_?)del	Pathogenic
1453304	NM_001201543.2(FAM161A):c.1177C>T (p.Gln393Ter)	Pathogenic
1454064	NM_001201543.2(FAM161A):c.1589C>G (p.Ser530Ter)	Pathogenic
1454588	NM_001201543.2(FAM161A):c.946G>T (p.Glu316Ter)	Pathogenic
1454639	NM_001201543.2(FAM161A):c.673del (p.Arg225fs)	Pathogenic

SpliceAI

1210 predictions. Top by Δscore:

Variant	Effect	Δscore
2:61826600:C:CC	acceptor_gain	1.0000
2:61835991:AAATT:A	donor_gain	1.0000
2:61838593:AAG:A	donor_gain	1.0000
2:61838600:AG:A	donor_gain	1.0000
2:61838600:AGC:A	donor_gain	1.0000
2:61838601:G:C	donor_gain	1.0000
2:61842117:CTTA:C	donor_loss	1.0000
2:61842118:TTACC:T	donor_loss	1.0000
2:61842119:TACCT:T	donor_loss	1.0000
2:61842120:A:AC	donor_gain	1.0000
2:61842120:A:T	donor_loss	1.0000
2:61842121:C:CC	donor_gain	1.0000
2:61842356:TCAGC:T	acceptor_gain	1.0000
2:61842357:CAGC:C	acceptor_gain	1.0000
2:61842357:CAGCC:C	acceptor_gain	1.0000
2:61842361:C:CC	acceptor_gain	1.0000
2:61842361:CTG:C	acceptor_loss	1.0000
2:61842362:T:C	acceptor_loss	1.0000
2:61853890:T:TA	donor_gain	1.0000
2:61826492:T:A	donor_gain	0.9900
2:61826595:TAAAG:T	acceptor_gain	0.9900
2:61827098:TGTTA:T	donor_loss	0.9900
2:61827099:GTTA:G	donor_loss	0.9900
2:61827100:TTACC:T	donor_loss	0.9900
2:61827101:TA:T	donor_loss	0.9900
2:61827102:A:C	donor_loss	0.9900
2:61827254:TTTTT:T	acceptor_gain	0.9900
2:61827259:C:CC	acceptor_gain	0.9900
2:61835985:G:C	donor_gain	0.9900
2:61836106:CTTT:C	acceptor_gain	0.9900

AlphaMissense

4724 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:61840278:A:C	F242L	0.994
2:61840278:A:T	F242L	0.994
2:61840280:A:G	F242L	0.994
2:61840158:G:C	F282L	0.990
2:61840158:G:T	F282L	0.990
2:61840160:A:G	F282L	0.990
2:61842231:C:G	A105P	0.986
2:61842239:A:G	L102S	0.986
2:61827240:C:G	A568P	0.983
2:61840386:A:C	F206L	0.983
2:61840386:A:T	F206L	0.983
2:61840388:A:G	F206L	0.983
2:61840397:A:G	W203R	0.983
2:61840397:A:T	W203R	0.983
2:61840023:A:C	F327L	0.981
2:61840023:A:T	F327L	0.981
2:61840025:A:G	F327L	0.981
2:61840144:A:T	V287D	0.981
2:61827252:C:G	A564P	0.980
2:61840263:T:A	R247S	0.980
2:61840263:T:G	R247S	0.980
2:61839939:A:C	F355L	0.978
2:61839939:A:T	F355L	0.978
2:61839941:A:G	F355L	0.978
2:61840395:C:A	W203C	0.978
2:61840395:C:G	W203C	0.978
2:61840029:A:C	F325L	0.977
2:61840029:A:T	F325L	0.977
2:61840031:A:G	F325L	0.977
2:61839436:C:G	R523P	0.975

dbSNP variants (sampled 300 via entrez): RS1000032185 (2:61804114 A>G), RS1000090502 (2:61804390 C>A,T), RS1000121249 (2:61847577 C>G), RS1000133441 (2:61845270 T>C), RS1000164882 (2:61823926 T>A), RS1000171613 (2:61843881 C>G,T), RS1000217803 (2:61826224 G>C), RS1000326342 (2:61819715 C>A,T), RS1000375752 (2:61832766 G>C), RS1000444173 (2:61854573 G>A), RS1000479160 (2:61825763 A>C,G), RS1000592528 (2:61819042 T>G), RS1000679100 (2:61834019 T>C), RS1000685359 (2:61808448 A>G), RS1000697956 (2:61825487 G>A)

Disease associations

OMIM: gene MIM:613596 | disease phenotypes: MIM:606068, MIM:268000, MIM:120970

GenCC curated gene-disease

Disease	Classification	Inheritance
retinitis pigmentosa 28	Definitive	Autosomal recessive
retinitis pigmentosa	Supportive	Autosomal dominant

Mondo (4): retinitis pigmentosa 28 (MONDO:0011630), inherited retinal dystrophy (MONDO:0019118), retinitis pigmentosa (MONDO:0019200), cone-rod dystrophy (MONDO:0015993)

Orphanet (3): OBSOLETE: Inherited retinal disorder (Orphanet:71862), Retinitis pigmentosa (Orphanet:791), Cone rod dystrophy (Orphanet:1872)

HPO phenotypes

34 total (30 of 34 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:0000510	Rod-cone dystrophy
HP:0000512	Abnormal electroretinogram
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:0001133	Constriction of peripheral visual field
HP:0007663	Reduced visual acuity
HP:0007675	Progressive night blindness
HP:0007703	Abnormal retinal pigmentation
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

4 associations (top):

Study	Trait	p-value
GCST005752_4	Systemic lupus erythematosus	1.000000e-06
GCST006061_164	Atrial fibrillation	2.000000e-09
GCST006956_8	Erectile dysfunction	8.000000e-06
GCST007400_2	Systemic lupus erythematosus	2.000000e-07

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
D000071700	Cone-Rod Dystrophies	C11.270.152; C11.768.585.658.250; C16.320.290.152
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

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	decreases expression, increases expression	3
Cadmium Chloride	increases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
FR900359	decreases phosphorylation	1
TAK-243	increases sumoylation	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
methylparaben	decreases expression	1
sulforaphane	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
abrine	decreases expression	1
eprenetapopt	affects expression, affects reaction	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	increases abundance, increases expression, affects cotreatment	1
Azathioprine	decreases expression	1
Estradiol	decreases reaction, increases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	affects expression	1
Smoke	increases abundance, increases expression	1
Dronabinol	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Valproic Acid	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

259 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