CABP4

Summary

CABP4 (calcium binding protein 4, HGNC:1386) is a protein-coding gene on chromosome 11q13.2, encoding Calcium-binding protein 4 (P57796). Involved in normal synaptic function through regulation of Ca(2+) influx and neurotransmitter release in photoreceptor synaptic terminals and in auditory transmission.

This gene encodes a member of the CABP family of calcium binding protein characterized by four EF-hand motifs. Mutations in this gene are associated with congenital stationary night blindness type 2B. Three transcript variants encoding two different isoforms have been found for this gene.

Source: NCBI Gene 57010 — RefSeq curated summary.

At a glance

• Gene–disease (curated): cone-rod synaptic disorder, congenital nonprogressive (Definitive, GenCC) — +2 more curated relationships
• GWAS associations: 5
• Clinical variants (ClinVar): 406 total — 19 pathogenic, 6 likely-pathogenic
• Phenotypes (HPO): 29
• Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
• MANE Select transcript: NM_145200

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1386
Approved symbol	CABP4
Name	calcium binding protein 4
Location	11q13.2
Locus type	gene with protein product
Status	Approved
Aliases	CSNB2B
Ensembl gene	ENSG00000175544
Ensembl biotype	protein_coding
OMIM	608965
Entrez	57010

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding_CDS_not_defined, 2 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000325656, ENST00000438189, ENST00000538060, ENST00000542025, ENST00000542233, ENST00000545040, ENST00000545777

RefSeq mRNA: 4 — MANE Select: NM_145200 NM_001300895, NM_001300896, NM_001379183, NM_145200

CCDS: CCDS73333, CCDS8166

Canonical transcript exons

ENST00000325656 — 6 exons

Exon	Start	End
ENSE00001185997	67458371	67458518
ENSE00001186007	67457573	67457682
ENSE00001186018	67456299	67456442
ENSE00001186032	67455354	67455789
ENSE00001287593	67456188	67456218
ENSE00003299163	67458631	67461752

Expression profiles

Bgee: expression breadth ubiquitous, 226 present calls, max score 90.96.

FANTOM5 (CAGE): breadth broad, TPM avg 0.4570 / max 29.6368, expressed in 205 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
115473	0.4201	199
115477	0.0139	5
115476	0.0099	3
115474	0.0086	5
115475	0.0045	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
vena cava	UBERON:0004087	90.96	gold quality
cardia of stomach	UBERON:0001162	90.77	gold quality
ventral tegmental area	UBERON:0002691	90.11	gold quality
cerebellar vermis	UBERON:0004720	89.99	gold quality
body of tongue	UBERON:0011876	89.90	gold quality
pericardium	UBERON:0002407	89.55	gold quality
subthalamic nucleus	UBERON:0001906	89.14	gold quality
dorsal plus ventral thalamus	UBERON:0001897	88.92	gold quality
inferior vagus X ganglion	UBERON:0005363	88.82	gold quality
lateral nuclear group of thalamus	UBERON:0002736	88.79	gold quality
tongue	UBERON:0001723	88.71	gold quality
pharyngeal mucosa	UBERON:0000355	88.45	gold quality
epithelium of nasopharynx	UBERON:0001951	88.12	silver quality
superficial temporal artery	UBERON:0001614	88.02	silver quality
mammary duct	UBERON:0001765	87.92	silver quality
saphenous vein	UBERON:0007318	87.88	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	87.85	silver quality
medulla oblongata	UBERON:0001896	87.66	gold quality
superior surface of tongue	UBERON:0007371	87.65	gold quality
pons	UBERON:0000988	87.23	silver quality
superior vestibular nucleus	UBERON:0007227	87.22	gold quality
lateral globus pallidus	UBERON:0002476	87.20	silver quality
sperm	CL:0000019	86.99	silver quality
trachea	UBERON:0003126	86.78	gold quality
pylorus	UBERON:0001166	86.60	gold quality
dorsal root ganglion	UBERON:0000044	86.37	gold quality
trigeminal ganglion	UBERON:0001675	86.36	gold quality
nipple	UBERON:0002030	86.32	silver quality
substantia nigra pars compacta	UBERON:0001965	85.64	silver quality
renal medulla	UBERON:0000362	85.60	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	43.67
E-GEOD-137537	yes	14.03
E-MTAB-3929	no	20.22
E-ANND-3	no	2.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

88 targeting CABP4, 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-6867-5P	100.00	82.21	3464
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-3162-3P	100.00	65.37	363
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-29B-2-5P	99.67	68.98	1726

Functional genomics

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

Literature-anchored findings (GeneRIF, showing 9)

• it is reported for the first time that mutations in CABP4 lead to autosomal recessive congenital stationary night blindness (PMID:16960802)
• A novel homozygous nonsense mutation in CABP4 in two siblings resulted in a phenotype with severely reduced cone function and only negligibly reduced rod function on electroretinography and psychophysical testing. (PMID:19074807)
• This report significantly expands on the phenotype associated with calcium binding protein 4 mutations. (PMID:20157620)
• Complex regulation of voltage-dependent activation and inactivation properties of retinal voltage-gated Cav1.4 L-type Ca2+ channels by Ca2+-binding protein 4 (CaBP4). (PMID:22936811)
• we found a homozygous compound mutation in the CABP4 gene in 3 patients with congenital stationary night blindess 2. (PMID:23714322)
• In this study, a novel compound heterozygous mutation, c.[1A>G]; [608G>T] (p.[0?]; p.[W203L]), was identified in the LRIT3 gene of a proband. No mutations were identified in the CABP4 or GPR179 gene. (PMID:27428514)
• Twenty-nine CACNA1F variations were detected among 34 families in the total cohort, and a novel CABP4 variation was identified in one family. (PMID:28002560)
• Foveal thinning is a feature of CABP4 retinopathy. Normal autofluorescence is consistent with inner retinal dysfunction and suggests the condition could be amenable to gene therapy. Retinal dysfunction was stable throughout follow-up. (PMID:28635425)
• CABP4-related retinal disease is a cone-rod system disorder with possible foveal abnormalities. (PMID:29525873)

Cross-species orthologs

15 orthologs

Organism	Symbol	Gene ID
danio_rerio	CABP4	ENSDARG00000105631
mus_musculus	Cabp4	ENSMUSG00000024842
rattus_norvegicus	Cabp4	ENSRNOG00000022044
drosophila_melanogaster	TpnC4	FBGN0033027
drosophila_melanogaster	CG13526	FBGN0034774
drosophila_melanogaster	CG5024	FBGN0039373
drosophila_melanogaster	CG17770	FBGN0039374
drosophila_melanogaster	CG30378	FBGN0050378
caenorhabditis_elegans		WBGENE00000285
caenorhabditis_elegans		WBGENE00000287
caenorhabditis_elegans	pat-10	WBGENE00003934
caenorhabditis_elegans		WBGENE00006583
caenorhabditis_elegans		WBGENE00008453
caenorhabditis_elegans	F35C12.3	WBGENE00009408
caenorhabditis_elegans		WBGENE00015264

Paralogs (20): CABP7 (ENSG00000100314), CABP5 (ENSG00000105507), CALML4 (ENSG00000129007), CALM2 (ENSG00000143933), CETN2 (ENSG00000147400), CETN3 (ENSG00000153140), CABP1 (ENSG00000157782), CALM3 (ENSG00000160014), CABP2 (ENSG00000167791), CALML6 (ENSG00000169885), EFCAB3 (ENSG00000172421), EFCAB12 (ENSG00000172771), CETN1 (ENSG00000177143), CALML3 (ENSG00000178363), CALML5 (ENSG00000178372), CALN1 (ENSG00000183166), CALM1 (ENSG00000198668), EFCAB2 (ENSG00000203666), EFCAB7 (ENSG00000203965), EFCAB9 (ENSG00000214360)

Protein

Protein identifiers

Calcium-binding protein 4 — P57796 (reviewed: P57796)

All UniProt accessions (2): P57796, F5H3E8

UniProt curated annotations — full annotation on UniProt →

Function. Involved in normal synaptic function through regulation of Ca(2+) influx and neurotransmitter release in photoreceptor synaptic terminals and in auditory transmission. Modulator of CACNA1D and CACNA1F, suppressing the calcium-dependent inactivation and shifting the activation range to more hyperpolarized voltages.

Subunit / interactions. Interacts with CACNA1F and CACNA1D (via IQ domain) in a calcium independent manner. Interacts (via N-terminus) with UNC119.

Subcellular location. Cytoplasm. Presynapse.

Tissue specificity. Expressed in retina and in the inner hair cells (IHC) of the cochlea.

Post-translational modifications. Phosphorylated. Phosphorylation levels change with the light conditions and regulate the activity.

Disease relevance. Cone-rod synaptic disorder, congenital non-progressive (CRSD) [MIM:610427] A non-progressive retinal disorder characterized by stable low vision, nystagmus, photophobia, a normal or near-normal fundus appearance, and no night blindness. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (2)

UniProt ID	Names	Canonical?
P57796-1	1	yes
P57796-2	2

RefSeq proteins (4): NP_001287824, NP_001287825, NP_001366112, NP_660201* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002048	EF_hand_dom	Domain
IPR011992	EF-hand-dom_pair	Homologous_superfamily
IPR018247	EF_Hand_1_Ca_BS	Binding_site
IPR043582	CaBP1/2/4/5	Family

Pfam: PF00036, PF13499

UniProt features (27 total): binding site 15, domain 4, splice variant 2, compositionally biased region 2, chain 1, modified residue 1, sequence variant 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P57796-F1	65.01	0.01

Functional residue map

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

Ligand- & substrate-binding residues (15): 146; 148; 153; 219; 221; 223; 225; 230; 256; 258; 260; 262 …

Post-translational modifications (1): 42

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 148 (showing top): GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, GOBP_PHOTOTRANSDUCTION, GOBP_NEUROGENESIS, GOBP_NEURAL_RETINA_DEVELOPMENT, chr11q13, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_EYE_PHOTORECEPTOR_CELL_DIFFERENTIATION, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, GOBP_PHOTORECEPTOR_CELL_DEVELOPMENT, GOBP_RESPONSE_TO_RADIATION, GOBP_CAMERA_TYPE_EYE_PHOTORECEPTOR_CELL_DIFFERENTIATION, GOBP_DETECTION_OF_LIGHT_STIMULUS, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_DETECTION_OF_ABIOTIC_STIMULUS, GOBP_PHOTORECEPTOR_CELL_DIFFERENTIATION

GO Biological Process (6): signal transduction (GO:0007165), visual perception (GO:0007601), phototransduction (GO:0007602), photoreceptor cell morphogenesis (GO:0008594), retinal cone cell development (GO:0046549), retinal bipolar neuron differentiation (GO:0060040)

GO Molecular Function (4): calcium channel regulator activity (GO:0005246), calcium ion binding (GO:0005509), transmembrane transporter binding (GO:0044325), metal ion binding (GO:0046872)

GO Cellular Component (7): extracellular region (GO:0005576), cytoplasm (GO:0005737), cytosol (GO:0005829), terminal bouton (GO:0043195), synapse (GO:0045202), cell projection (GO:0042995), presynapse (GO:0098793)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
sensory perception of light stimulus	1
signal transduction	1
detection of light stimulus	1
photoreceptor cell development	1
cell morphogenesis involved in neuron differentiation	1
eye photoreceptor cell development	1
retinal cone cell differentiation	1
neural retina development	1
retina morphogenesis in camera-type eye	1
glutamatergic neuron differentiation	1
calcium channel activity	1
ion channel regulator activity	1
metal ion binding	1
protein binding	1
cation binding	1
intracellular anatomical structure	1
cytoplasm	1
axon terminus	1
presynapse	1
cell junction	1
synapse	1

Protein interactions and networks

STRING

1883 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CABP4	CACNA1F	O60840	968
CABP4	S100G	P29377	858
CABP4	NYX	Q9GZU5	837
CABP4	LRIT3	Q3SXY7	756
CABP4	CTBP2	P56545	698
CABP4	GPR179	Q6PRD1	695
CABP4	CACNA2D4	Q7Z3S7	693
CABP4	CACNA1D	Q01668	689
CABP4	SLC24A1	O60721	683
CABP4	S100A6	P06703	680
CABP4	GRM6	O15303	662
CABP4	TRPM1	Q7Z4N2	661
CABP4	RDH5	Q92781	626
CABP4	PDE6B	P35913	615
CABP4	GNAT1	P11488	612

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CABP4	MFHAS1	psi-mi:“MI:0407”(direct interaction)	0.440
CABP4	SPTB	psi-mi:“MI:0914”(association)	0.350

BioGRID (11): CACNA1F (Reconstituted Complex), AES (Two-hybrid), IKZF3 (Two-hybrid), BCL6 (Two-hybrid), LNX2 (Two-hybrid), CABP4 (Reconstituted Complex), DCAF6 (Affinity Capture-MS), SPTB (Affinity Capture-MS), CALM2 (Negative Genetic), CALM3 (Negative Genetic), SERBP1 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A5PKJ4, A6QQJ8, D3YZU1, D3ZD05, D3ZG83, O88888, O95382, P0C865, P57796, Q02779, Q13470, Q13938, Q16584, Q1LZH7, Q2PS20, Q2TBQ9, Q4ACU6, Q5R8E2, Q5ZM14, Q63ZY3, Q66HA1, Q66L42, Q68G30, Q69FB3, Q6P597, Q6P9Q4, Q7TSG2, Q80WT0, Q80XI6, Q8BX02, Q8HZJ4, Q8K031, Q8VHC5, Q91W40, Q96JJ6, Q96L34, Q99ML2, Q9BR39, Q9BYB0, Q9D4J1

Diamond homologs: A0A125YHX7, A0A125YZN2, A2WN93, A2Y609, A3E3H0, A3E4D8, A3E4F9, A4UHC0, A8CEP3, A8I1Q0, D2DGW3, J9W034, O15182, O23184, O35648, O49717, O60041, O74435, O82018, O82659, O94739, P02597, P02598, P04352, P04353, P04464, P05419, P05434, P06704, P06707, P06708, P06787, P0DH95, P0DH96, P11120, P15094, P15159, P17928, P21797, P25071

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	19
Likely pathogenic	6
Uncertain significance	212
Likely benign	101
Benign	30

Top pathogenic / likely-pathogenic (25)

Variant ID	HGVS	Classification
1007462	NM_145200.5(CABP4):c.692T>C (p.Leu231Pro)	Pathogenic
1069487	NM_145200.5(CABP4):c.154C>T (p.Arg52Ter)	Pathogenic
1075268	NM_145200.5(CABP4):c.370del (p.Arg124fs)	Pathogenic
1076898	NM_145200.5(CABP4):c.739G>T (p.Glu247Ter)	Pathogenic
1345948	NM_145200.5(CABP4):c.366+1G>T	Pathogenic
1383967	NM_145200.5(CABP4):c.66dup (p.Ala23fs)	Pathogenic
1454901	NM_145200.5(CABP4):c.397+2T>A	Pathogenic
1454902	NM_145200.5(CABP4):c.541+1G>T	Pathogenic
190959	NM_145200.5(CABP4):c.646C>T (p.Arg216Ter)	Pathogenic
190960	NM_145200.5(CABP4):c.81_82insA (p.Pro28fs)	Pathogenic
2006829	NM_145200.5(CABP4):c.339dup (p.Pro114fs)	Pathogenic
2036528	NM_145200.5(CABP4):c.584dup (p.Leu198fs)	Pathogenic
2038276	NM_145200.5(CABP4):c.233_234del (p.Glu78fs)	Pathogenic
3635045	NM_145200.5(CABP4):c.24dup (p.Gln9fs)	Pathogenic
438047	NM_145200.5(CABP4):c.673C>T (p.Arg225Ter)	Pathogenic
4744253	NM_145200.5(CABP4):c.415G>T (p.Glu139Ter)	Pathogenic
4799303	NM_145200.5(CABP4):c.505G>T (p.Glu169Ter)	Pathogenic
635475	NM_145200.5(CABP4):c.61_62delinsA (p.Pro21fs)	Pathogenic
872443	NM_145200.5(CABP4):c.457dup (p.Glu153fs)	Pathogenic
1477513	NM_145200.5(CABP4):c.371G>A (p.Arg124His)	Likely pathogenic
3769566	NM_145200.5(CABP4):c.256del (p.Ala86fs)	Likely pathogenic
438232	NM_145200.5(CABP4):c.800-18_*795del	Likely pathogenic
838524	NM_145200.5(CABP4):c.652-2A>G	Likely pathogenic
844856	NM_145200.5(CABP4):c.542-2A>C	Likely pathogenic
967055	NM_145200.5(CABP4):c.542-17_542-2delinsGCCCACCATT	Likely pathogenic

SpliceAI

860 predictions. Top by Δscore:

Variant	Effect	Δscore
11:67455786:G:GT	donor_gain	1.0000
11:67455787:A:T	donor_gain	1.0000
11:67456415:G:GT	donor_gain	1.0000
11:67456435:G:GT	donor_gain	1.0000
11:67456436:A:G	donor_gain	1.0000
11:67456438:GCGCA:G	donor_gain	1.0000
11:67456440:GCA:G	donor_gain	1.0000
11:67456443:G:GG	donor_gain	1.0000
11:67456447:G:GG	donor_gain	1.0000
11:67456487:G:GT	donor_gain	1.0000
11:67457563:G:A	acceptor_gain	1.0000
11:67457571:A:AG	acceptor_gain	1.0000
11:67457571:AGTG:A	acceptor_gain	1.0000
11:67457572:G:GG	acceptor_gain	1.0000
11:67457572:GT:G	acceptor_gain	1.0000
11:67457572:GTGG:G	acceptor_gain	1.0000
11:67458516:ACGG:A	donor_loss	1.0000
11:67458518:GGT:G	donor_loss	1.0000
11:67458629:A:AG	acceptor_gain	1.0000
11:67458630:G:GG	acceptor_gain	1.0000
11:67458630:GA:G	acceptor_gain	1.0000
11:67455753:GACA:G	donor_gain	0.9900
11:67455786:G:T	donor_gain	0.9900
11:67455791:T:G	donor_gain	0.9900
11:67456297:A:AG	acceptor_gain	0.9900
11:67456298:G:GG	acceptor_gain	0.9900
11:67456298:GA:G	acceptor_gain	0.9900
11:67456298:GAGC:G	acceptor_gain	0.9900
11:67456415:G:T	donor_gain	0.9900
11:67456441:CAG:C	donor_loss	0.9900

AlphaMissense

1789 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:67456313:T:C	F138L	0.996
11:67456315:C:A	F138L	0.996
11:67456315:C:G	F138L	0.996
11:67457674:T:C	F215L	0.995
11:67457676:C:A	F215L	0.995
11:67457676:C:G	F215L	0.995
11:67456322:T:C	F141L	0.994
11:67456324:T:A	F141L	0.994
11:67456324:T:G	F141L	0.994
11:67458396:T:C	I226T	0.994
11:67456410:T:C	L170P	0.992
11:67457599:T:C	F190L	0.992
11:67457601:T:A	F190L	0.992
11:67457601:T:G	F190L	0.992
11:67457675:T:C	F215S	0.992
11:67458633:T:C	F268L	0.992
11:67458635:T:A	F268L	0.992
11:67458635:T:G	F268L	0.992
11:67456377:G:C	R159P	0.989
11:67457600:T:C	F190S	0.989
11:67456395:C:A	P165H	0.988
11:67456302:T:C	L134P	0.987
11:67458396:T:G	I226S	0.986
11:67456314:T:C	F138S	0.985
11:67456386:G:T	G162V	0.985
11:67456398:C:T	T166I	0.985
11:67457672:C:A	A214D	0.984
11:67456394:C:T	P165S	0.983
11:67458396:T:A	I226N	0.983
11:67456347:T:A	I149N	0.982

dbSNP variants (sampled 300 via entrez): RS1000441051 (11:67460577 A>G), RS1000811992 (11:67460798 C>T), RS1000829672 (11:67453427 C>A), RS1001605836 (11:67460853 C>T), RS1002268917 (11:67452439 G>A,C), RS1002291533 (11:67458412 G>A), RS1002333604 (11:67450885 G>A,C), RS1002928514 (11:67455152 C>T), RS1003041156 (11:67460984 C>G,T), RS1003199431 (11:67454310 C>T), RS1003504971 (11:67452192 T>C), RS1003834380 (11:67456791 C>T), RS1003935148 (11:67451335 C>A,T), RS1004538195 (11:67454845 C>G,T), RS1004606330 (11:67460114 A>G)

Disease associations

OMIM: gene MIM:608965 | disease phenotypes: MIM:610427, MIM:310500, MIM:120970, MIM:300600, MIM:276900

GenCC curated gene-disease

Disease	Classification	Inheritance
cone-rod synaptic disorder, congenital nonprogressive	Definitive	Autosomal recessive
congenital stationary night blindness	Supportive	Autosomal dominant
autosomal dominant nocturnal frontal lobe epilepsy	Supportive	Autosomal dominant

Mondo (11): cone-rod synaptic disorder, congenital nonprogressive (MONDO:0012490), inherited retinal dystrophy (MONDO:0019118), congenital stationary night blindness (MONDO:0016293), eye disorder (MONDO:0005328), cone-rod dystrophy (MONDO:0015993), achromatopsia (MONDO:0018852), optic atrophy (MONDO:0003608), cone dystrophy (MONDO:0000455), Aland island eye disease (MONDO:0010371), Usher syndrome (MONDO:0019501), (MONDO:0020300)

Orphanet (7): Congenital stationary night blindness (Orphanet:215), OBSOLETE: Inherited retinal disorder (Orphanet:71862), Cone rod dystrophy (Orphanet:1872), Achromatopsia (Orphanet:49382), Progressive cone dystrophy (Orphanet:1871), Åland Islands eye disease (Orphanet:178333), Usher syndrome (Orphanet:886)

HPO phenotypes

29 total (30 of 29 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000020	Urinary incontinence
HP:0000486	Strabismus
HP:0000505	Visual impairment
HP:0000551	Color vision defect
HP:0000613	Photophobia
HP:0000639	Nystagmus
HP:0000708	Atypical behavior
HP:0000716	Depression
HP:0000733	Motor stereotypy
HP:0000739	Anxiety
HP:0001256	Mild intellectual disability
HP:0001345	Psychotic mentation
HP:0002069	Bilateral tonic-clonic seizure
HP:0002268	Paroxysmal dystonia
HP:0002883	Hyperventilation
HP:0004305	Involuntary movements
HP:0007018	Attention deficit hyperactivity disorder
HP:0007642	Early-onset non-progressive night blindness
HP:0007984	ERG: Reduced dark-adapted b-wave amplitude
HP:0011174	Focal hyperkinetic seizure
HP:0011182	Interictal epileptiform activity
HP:0011193	EEG with focal spikes
HP:0025235	NREM parasomnia
HP:0025236	Sleep walking
HP:0031535	Increased theta frequency activity in EEG
HP:0031589	Suicidal ideation
HP:0031951	Nocturnal seizures
HP:0100543	Cognitive impairment
HP:0000556	Retinal dystrophy

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST004602_198	Mean corpuscular volume	6.000000e-22
GCST004602_199	Mean corpuscular volume	1.000000e-13
GCST010002_241	Refractive error	3.000000e-13
GCST90002392_352	Mean corpuscular volume	2.000000e-11
GCST90002396_471	Mean reticulocyte volume	2.000000e-16

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010701	mean reticulocyte volume

MeSH disease descriptors (8)

Descriptor	Name	Tree numbers
D000077765	Cone Dystrophy	C11.270.151; C11.768.216
D000071700	Cone-Rod Dystrophies	C11.270.152; C11.768.585.658.250; C16.320.290.152
D005128	Eye Diseases	C11
D009896	Optic Atrophy	C10.292.700.225; C11.640.451
D058499	Retinal Dystrophies	C11.768.585.658
D052245	Usher Syndromes	C09.218.458.341.186.500.500; C09.218.458.341.887.886; C10.597.751.418.341.186.500.500; C10.597.751.418.341.887.886; C10.597.751.941.162.625.500; C11.768.585.658.500.813; C11.966.075.375.500; C16.131.077.299.500; C16.320.290.684.500; C23.888.592.763.393.341.887.886
C562664	Aland Island Eye Disease (supp.)
C536122	Night blindness, congenital stationary (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol F	affects cotreatment, decreases expression	1
bisphenol A	affects expression	1
sodium arsenite	increases expression	1
fipronil	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
DEET	affects cotreatment, decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Diethylhexyl Phthalate	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Zinc Sulfate	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00911924	PHASE4	COMPLETED	A Prospective, Unmasked Evaluation of the iStent in Patients With Primary Open-Angle Glaucoma
NCT00913029	PHASE4	COMPLETED	Evaluation of the iStent Versus Two Ocular Hypotensive Agents in Patients With Primary Open-angle Glaucoma (POAG)
NCT00957190	PHASE4	COMPLETED	The DIOXXACT Trial(Diurnal IOP and OBF Xalatan vs Xalatan And Cosopt Trial)
NCT03148132	PHASE4	COMPLETED	VEGF Concentrations After Intravitreal Bevacizumab vs Ranibizumab as a Treatment for Type 1 ROP
NCT07266948	PHASE4	RECRUITING	Impact of TRYPTYR on a Patient’s Quality of Life and Ability to Perform Work
NCT07267299	PHASE4	NOT_YET_RECRUITING	Switching From Restasis to TRYPTYR
NCT07267481	PHASE4	NOT_YET_RECRUITING	Switching From Xiidra to TRYPTYR
NCT07434635	PHASE4	RECRUITING	APPRAISE: Assessment of Pain and Posterior Synechiae Reduction With Atropine, an Investigation of Post-Surgical Eyes
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
NCT00120432	PHASE3	COMPLETED	Single Dose of 1% Tropicamide and 10% Phenylephrine for Pupillary Dilation
NCT00333203	PHASE3	COMPLETED	Next Generation Ophthalmic Irrigating Solution Posterior Segment Study
NCT02157077	PHASE3	COMPLETED	Aflibercept After Ranibizumab in Exudative Age-related Macular Degeneration
NCT03954626	PHASE3	COMPLETED	Study to Collect Safety and ECG Data on Brolucizumab 6 mg Intravitreal Treatment in Patients With Wet AMD
NCT04149210	PHASE3	COMPLETED	FLuorometholone as Adjunctive MEdical Therapy for TT Surgery (FLAME) Trial
NCT04663750	PHASE3	RECRUITING	Vitrectomy, Subretinal Tissue Plasminogen Activator (TPA) and Intravitreal Gas for Submacular Haemorrhage Secondary to Exudative (Wet) Age-related Macular Degeneration (TIGER).
NCT05158699	PHASE3	TERMINATED	Effectiveness of Periocular Drug Injection in CATaract Surgery
NCT05656027	PHASE3	COMPLETED	Phase 3 Evaluation of the Safety and Efficacy of LNZ100 & LNZ101 for the Treatment of Presbyopia
NCT05728944	PHASE3	COMPLETED	Phase 3 Efficacy Study of LNZ100 & LNZ101 for the Treatment of Presbyopia
NCT05753189	PHASE3	COMPLETED	Phase 3 Safety Study of LNZ100 and LNZ101 for the Treatment of Presbyopia Subjects
NCT06045299	PHASE3	COMPLETED	Evaluation of the Efficacy and Safety of LNZ101 and LNZ100 for the Presbyopia
NCT06601101	PHASE3	RECRUITING	Effects of Topical Insulin on Corneal Epithelium Healing After Corneal Crosslinking in Patients With Keratoconus
NCT06891443	PHASE3	RECRUITING	Study to Evaluate Sepofarsen in Subjects With Leber Congenital Amaurosis (LCA) Type 10 (HYPERION)
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]
NCT00123279	PHASE2	COMPLETED	Intravitreal Microplasmin in Patients Undergoing Surgical Vitrectomy
NCT00211432	PHASE2	COMPLETED	Treatment of Pseudovitellium Detachment With Open-Label Anecortave Acetate Sterile Suspension (15 mg)
NCT00315640	PHASE2	COMPLETED	Anecortave Acetate for Treatment of Steroid Induced Intraocular Pressure (IOP) Elevation
NCT01016873	PHASE2	COMPLETED	INTREPID - IRay Plus Anti-VEGF Treatment For Patients With Wet AMD
NCT01399515	PHASE2	COMPLETED	Efficacy and Safety of Oral Valproic Acid for Retinitis Pigmentosa
NCT01521065	PHASE2	UNKNOWN	An Open-label Study to Evaluate the Clinical and Economic Benefits of I-Ray in Patients With Choroidal Neovascularization Secondary to Age-related Macular Degeneration
NCT01693315	PHASE2	COMPLETED	Multiple Dose-escalation Study of AMA0076 in Patients With Ocular Hypertension or Primary Open-angle Glaucoma
NCT02136940	PHASE2	COMPLETED	Multiple Dose-parallel-group Study of AMA0076 in Patients With Primary Open-Angle Glaucoma or Ocular Hypertension
NCT02348359	PHASE2	TERMINATED	X-82 to Treat Age-related Macular Degeneration
NCT03029104	PHASE2	TERMINATED	Collagen Cross-Linking With Ultraviolet-A in Asymmetric Corneas
NCT03871361	PHASE2	COMPLETED	Abatacept in Patients With Birdshot HLA A29 Uveitis
NCT05294328	PHASE2	COMPLETED	Evaluation of the Safety and Effectiveness of Aceclidine/Brimonidine (LNZ101) and Aceclidine (LNZ100) in the Treatment of Presbyopia
NCT05431543	PHASE2	COMPLETED	Evaluation of the Safety and Effectiveness of Aceclidine (LNZ101) and Aceclidine + Brimonidine (LNZ100) in the Treatment of Presbyopia
NCT05814757	PHASE2	COMPLETED	OTX-DED for the Short-term Treatment of the Symptoms of Dry Eye Disease (DED)