SLC24A1

Summary

SLC24A1 (solute carrier family 24 member 1, HGNC:10975) is a protein-coding gene on chromosome 15q22.31, encoding Sodium/potassium/calcium exchanger 1 (O60721). Calcium, potassium:sodium antiporter that transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+).

This gene encodes a member of the potassium-dependent sodium/calcium exchanger protein family. The encoded protein plays an important role in sodium/calcium exchange in retinal rod and cone photoreceptors by mediating the extrusion of one calcium ion and one potassium ion in exchange for four sodium ions. Mutations in this gene may play a role in congenital stationary night blindness. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 9187 — RefSeq curated summary.

At a glance

• Gene–disease (curated): inherited retinal dystrophy (Definitive, ClinGen) — +2 more curated relationships
• GWAS associations: 4
• Clinical variants (ClinVar): 776 total — 33 pathogenic, 8 likely-pathogenic
• Phenotypes (HPO): 6
• Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
• MANE Select transcript: NM_004727

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10975
Approved symbol	SLC24A1
Name	solute carrier family 24 member 1
Location	15q22.31
Locus type	gene with protein product
Status	Approved
Aliases	NCKX1, NCKX, RODX, KIAA0702, HsT17412, CSNB1D
Ensembl gene	ENSG00000074621
Ensembl biotype	protein_coding
OMIM	603617
Entrez	9187

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 3 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000261892, ENST00000339868, ENST00000399033, ENST00000425561, ENST00000434116, ENST00000449142, ENST00000505666, ENST00000535950, ENST00000537259, ENST00000539516, ENST00000544319, ENST00000546330, ENST00000929535

RefSeq mRNA: 6 — MANE Select: NM_004727 NM_001254740, NM_001301031, NM_001301032, NM_001301033, NM_001411142, NM_004727

CCDS: CCDS45284, CCDS73742, CCDS73743, CCDS73744, CCDS92023

Canonical transcript exons

ENST00000261892 — 10 exons

Exon	Start	End
ENSE00000943048	65638128	65638181
ENSE00001483848	65653830	65656260
ENSE00003458816	65623955	65625970
ENSE00003488644	65639595	65639703
ENSE00003497834	65651670	65651759
ENSE00003518252	65644427	65644513
ENSE00003553177	65645612	65645703
ENSE00003621874	65650382	65650942
ENSE00003648983	65652642	65652808
ENSE00003850459	65621938	65622092

Expression profiles

Bgee: expression breadth ubiquitous, 220 present calls, max score 85.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.4010 / max 174.9431, expressed in 1762 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
147235	7.6885	1755
147240	0.3712	105
147238	0.1571	7
147242	0.0948	36
147241	0.0505	20
147243	0.0249	8
147239	0.0104	3
147237	0.0037	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	85.60	silver quality
sural nerve	UBERON:0015488	85.33	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.17	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.36	gold quality
stromal cell of endometrium	CL:0002255	80.63	gold quality
visceral pleura	UBERON:0002401	80.47	gold quality
pigmented layer of retina	UBERON:0001782	79.30	gold quality
retina	UBERON:0000966	79.29	gold quality
parietal pleura	UBERON:0002400	79.25	gold quality
pleura	UBERON:0000977	79.15	gold quality
right uterine tube	UBERON:0001302	78.47	gold quality
tibia	UBERON:0000979	78.09	gold quality
endometrium	UBERON:0001295	78.09	gold quality
gall bladder	UBERON:0002110	77.98	gold quality
colonic epithelium	UBERON:0000397	77.91	gold quality
thyroid gland	UBERON:0002046	77.73	gold quality
left lobe of thyroid gland	UBERON:0001120	77.52	gold quality
right lobe of thyroid gland	UBERON:0001119	77.25	gold quality
ovary	UBERON:0000992	76.98	gold quality
calcaneal tendon	UBERON:0003701	76.81	gold quality
left ovary	UBERON:0002119	76.62	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	76.53	gold quality
adrenal tissue	UBERON:0018303	75.78	gold quality
bronchial epithelial cell	CL:0002328	75.48	gold quality
adipose tissue	UBERON:0001013	75.32	gold quality
endocervix	UBERON:0000458	75.21	gold quality
right adrenal gland	UBERON:0001233	75.19	gold quality
uterus	UBERON:0000995	75.10	gold quality
connective tissue	UBERON:0002384	75.10	gold quality
adipose tissue of abdominal region	UBERON:0007808	75.09	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	39.77
E-GEOD-137537	yes	14.78
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

76 targeting SLC24A1, 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-3613-3P	100.00	76.36	7965
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-4755-5P	99.71	70.34	2716

Functional genomics

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

Literature-anchored findings (GeneRIF, showing 3)

• A mutation in SLC24A1 is implicated in autosomal-recessive congenital stationary night blindness. (PMID:20850105)
• The index patient and his affected brother carry a homozygous single-nucleotide variants (SNVs) in sodium-calcium, potassium exchanger (SLC24A1) (c.2401G > T). (PMID:26822852)
• We report the association of many previously unreported variants with retinal disease, as well as new disease phenotypes associated with known genes, including the first association of the SLC24A1 gene with retinitis pigmentosa (PMID:27624628)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc24a1	ENSDARG00000041431
mus_musculus	Slc24a1	ENSMUSG00000034452
rattus_norvegicus	Slc24a1	ENSRNOG00000052051
drosophila_melanogaster	Nckx30C	FBGN0028704
caenorhabditis_elegans	ncx-4	WBGENE00003569
caenorhabditis_elegans		WBGENE00003570

Paralogs (4): SLC24A4 (ENSG00000140090), SLC24A2 (ENSG00000155886), SLC24A3 (ENSG00000185052), SLC24A5 (ENSG00000188467)

Protein

Protein identifiers

Sodium/potassium/calcium exchanger 1 — O60721 (reviewed: O60721)

Alternative names: Na(+)/K(+)/Ca(2+)-exchange protein 1, Retinal rod Na-Ca+K exchanger, Solute carrier family 24 member 1

All UniProt accessions (4): O60721, F5H127, F5H483, H0YH06

UniProt curated annotations — full annotation on UniProt →

Function. Calcium, potassium:sodium antiporter that transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+). Critical component of the visual transduction cascade, controlling the calcium concentration of outer segments during light and darkness. Light causes a rapid lowering of cytosolic free calcium in the outer segment of both retinal rod and cone photoreceptors and the light-induced lowering of calcium is caused by extrusion via this protein which plays a key role in the process of light adaptation.

Subcellular location. Cell membrane.

Tissue specificity. Expressed in the retina, particularly in the inner segment, outer and inner nuclear layers, and ganglion cell layer.

Post-translational modifications. The uncleaved signal sequence is required for efficient membrane targeting and proper membrane integration.

Disease relevance. Night blindness, congenital stationary, 1D (CSNB1D) [MIM:613830] An autosomal recessive form of congenital stationary night blindness, a non-progressive retinal disorder characterized by impaired night vision. CSNB1D is characterized by a Riggs type of electroretinogram (proportionally reduced a- and b-waves). Patients have visual acuity within the normal range and no symptoms of myopia and/or nystagmus. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the Ca(2+):cation antiporter (CaCA) (TC 2.A.19) family. SLC24A subfamily.

Isoforms (3)

UniProt ID	Names	Canonical?
O60721-1	1	yes
O60721-2	2
O60721-3	3

RefSeq proteins (6): NP_001241669, NP_001287960, NP_001287961, NP_001287962, NP_001398071, NP_004718* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004481	K/Na/Ca-exchanger	Family
IPR004817	SLC24A1	Family
IPR004837	NaCa_Exmemb	Domain
IPR044880	NCX_ion-bd_dom_sf	Homologous_superfamily

Pfam: PF01699

Catalyzed reactions (Rhea), 1 shown:

• Ca(2+)(out) + K(+)(out) + 4 Na(+)(in) = Ca(2+)(in) + K(+)(in) + 4 Na(+)(out) (RHEA:69967)

UniProt features (45 total): topological domain 12, transmembrane region 11, compositionally biased region 5, region of interest 4, sequence variant 3, repeat 2, modified residue 2, splice variant 2, chain 1, signal peptide 1, glycosylation site 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O60721-F1	55.56	0.16

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): 658, 724

Glycosylation sites (1): 290

Function

Pathways and Gene Ontology

Reactome pathways

12 pathways

ID	Pathway
R-HSA-2485179	Activation of the phototransduction cascade
R-HSA-425561	Sodium/Calcium exchangers
R-HSA-5619077	Defective SLC24A1 causes congenital stationary night blindness 1D (CSNB1D)
R-HSA-1643685	Disease
R-HSA-2187338	Visual phototransduction
R-HSA-2514856	The phototransduction cascade
R-HSA-382551	Transport of small molecules
R-HSA-425393
R-HSA-425407	SLC-mediated transmembrane transport
R-HSA-5619102	SLC transporter disorders
R-HSA-5619115	Disorders of transmembrane transporters
R-HSA-9709957	Sensory Perception

MSigDB gene sets: 268 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, MORF_RAGE, GOBP_POTASSIUM_ION_TRANSPORT, RNGTGGGC_UNKNOWN, WANG_CLIM2_TARGETS_UP, MODULE_162, GOBP_SODIUM_ION_TRANSMEMBRANE_TRANSPORT, MORF_ATRX, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_MONOATOMIC_CATION_TRANSPORT, GOBP_CELL_CELL_SIGNALING, GOBP_REGULATION_OF_SYNAPTIC_PLASTICITY, GOBP_LONG_TERM_SYNAPTIC_DEPRESSION, GOBP_CALCIUM_ION_IMPORT, GOBP_NEGATIVE_REGULATION_OF_SYNAPTIC_TRANSMISSION

GO Biological Process (14): monoatomic ion transport (GO:0006811), calcium ion transport (GO:0006816), intracellular calcium ion homeostasis (GO:0006874), visual perception (GO:0007601), response to light intensity (GO:0009642), sodium ion transmembrane transport (GO:0035725), long-term synaptic potentiation (GO:0060291), long-term synaptic depression (GO:0060292), calcium ion transmembrane transport (GO:0070588), potassium ion transmembrane transport (GO:0071805), calcium ion import across plasma membrane (GO:0098703), potassium ion transport (GO:0006813), sodium ion transport (GO:0006814), transmembrane transport (GO:0055085)

GO Molecular Function (5): calcium channel activity (GO:0005262), calcium, potassium:sodium antiporter activity (GO:0008273), symporter activity (GO:0015293), protein binding (GO:0005515), antiporter activity (GO:0015297)

GO Cellular Component (4): plasma membrane (GO:0005886), membrane (GO:0016020), outer membrane (GO:0019867), neuronal cell body (GO:0043025)

Reactome top-level categories

Rollup of top-8 pathways:

Category	Pathways
The phototransduction cascade	1
Metal ion SLC transporters	1
SLC transporter disorders	1
Sensory Perception	1
Visual phototransduction	1
Transport of small molecules	1
Disorders of transmembrane transporters	1
Disease	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
metal ion transport	3
monoatomic cation transmembrane transport	3
transport	2
regulation of synaptic plasticity	2
secondary active transmembrane transporter activity	2
membrane	2
intracellular monoatomic cation homeostasis	1
calcium ion homeostasis	1
sensory perception of light stimulus	1
response to light stimulus	1
sodium ion transport	1
positive regulation of synaptic transmission	1
negative regulation of synaptic transmission	1
calcium ion transport	1
potassium ion transport	1
calcium ion import	1
calcium ion transmembrane import into cytosol	1
inorganic cation import across plasma membrane	1
calcium ion import into cytosol	1
cellular process	1
monoatomic cation channel activity	1
calcium ion transmembrane transporter activity	1
calcium:sodium antiporter activity	1
solute:potassium antiporter activity	1
binding	1
cell periphery	1
cellular anatomical structure	1
somatodendritic compartment	1
cell body	1

Protein interactions and networks

STRING

1064 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC24A1	CNGA1	P29973	684
SLC24A1	CABP4	P57796	683
SLC24A1	CNGB1	Q14028	667
SLC24A1	PDE6B	P35913	667
SLC24A1	PDE6A	P16499	647
SLC24A1	LRIT3	Q3SXY7	641
SLC24A1	RCVRN	P35243	626
SLC24A1	GNAT1	P11488	616
SLC24A1	SLC8A1	P32418	615
SLC24A1	GNAT2	P19087	608
SLC24A1	CNGB3	Q9NQW8	603
SLC24A1	GRK7	Q8WTQ7	595
SLC24A1	CNGA3	Q16281	593
SLC24A1	PDE6C	P51160	592
SLC24A1	GNGT1	P63211	580

IntAct

8 interactions, top by confidence:

A	B	Type	Score
SLC24A1	ABL1	psi-mi:“MI:0915”(physical association)	0.400
SLC24A1	FYN	psi-mi:“MI:0915”(physical association)	0.400
GRB2	SLC24A1	psi-mi:“MI:0915”(physical association)	0.400
SLC24A1	NCK1	psi-mi:“MI:0915”(physical association)	0.400
PIK3R1	SLC24A1	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (4): SLC24A1 (Affinity Capture-RNA), SLC24A1 (Affinity Capture-Western), CNGA1 (Affinity Capture-Western), C1orf27 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A2R8Y7Y5, A4FU49, B2RTN2, I3L273, J3KML8, O00592, O35930, O46598, O60721, P07359, P23471, P23515, P97808, Q1ECS6, Q28256, Q28983, Q29RT9, Q2EG98, Q3MIW9, Q3TNW5, Q3V1M1, Q3V3Q4, Q4R729, Q58Y74, Q5FVR0, Q5XI99, Q62170, Q63912, Q6MG22, Q6U7R4, Q6WRH9, Q6WRI0, Q7Z7G0, Q80XH2, Q8BHE4, Q8BUE7, Q8JZQ0, Q8N5Q1, Q8R1W8, Q8TCU4

Diamond homologs: F1NXU8, O04034, O60721, Q49SH1, Q6AXS0, Q6J4K2, Q71RS6, Q925Q3, Q9FKP1, Q9FKP2, B8K1V7, O22252, O54701, P23685, P32418, P48765, P48766, P48767, P48768, P57103, P70414, P70549, Q01728, Q2R041, Q6H641, Q8BUN9, Q8CGQ8, Q8K596, Q8NFF2, Q99PD7, Q9EPQ0, Q9HC58, Q9UI40, Q9UPR5, Q9VDG5, Q9VN12, S4R2P9, O46383, Q28139, Q91WD8

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
SLC24A1	“down-regulates quantity”	calcium(2+)	relocalization
SLC24A1	“down-regulates quantity”	potassium(1+)	relocalization
SLC24A1	“up-regulates quantity”	sodium(1+)	relocalization

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	33
Likely pathogenic	8
Uncertain significance	463
Likely benign	207
Benign	29

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1068778	NM_004727.3(SLC24A1):c.1963C>T (p.Arg655Ter)	Pathogenic
1072566	NM_004727.3(SLC24A1):c.1325del (p.Pro442fs)	Pathogenic
1073610	NC_000015.9:g.(?65930466)(65932041_?)del	Pathogenic
1319075	NM_004727.3(SLC24A1):c.2948C>G (p.Ser983Ter)	Pathogenic
1350484	NM_004727.3(SLC24A1):c.1108A>T (p.Lys370Ter)	Pathogenic
1352702	NM_004727.3(SLC24A1):c.162_169del (p.Ser56fs)	Pathogenic
1378613	NM_004727.3(SLC24A1):c.836dup (p.Asn279fs)	Pathogenic
1425174	NM_004727.3(SLC24A1):c.2371G>T (p.Gly791Ter)	Pathogenic
1444567	NM_004727.3(SLC24A1):c.1664G>A (p.Trp555Ter)	Pathogenic
1451196	NM_004727.3(SLC24A1):c.1801A>T (p.Lys601Ter)	Pathogenic
1451529	NM_004727.3(SLC24A1):c.137dup (p.Leu47fs)	Pathogenic
1454862	NM_004727.3(SLC24A1):c.2794G>T (p.Glu932Ter)	Pathogenic
1456528	NM_004727.3(SLC24A1):c.600C>G (p.Tyr200Ter)	Pathogenic
1922108	NM_004727.3(SLC24A1):c.1094G>A (p.Trp365Ter)	Pathogenic
1937462	NM_004727.3(SLC24A1):c.2677_2699del (p.Asn893fs)	Pathogenic
2006786	NM_004727.3(SLC24A1):c.1940del (p.Leu647fs)	Pathogenic
2133742	NM_004727.3(SLC24A1):c.494dup (p.Tyr166fs)	Pathogenic
2736224	NM_004727.3(SLC24A1):c.2679del (p.Asn893fs)	Pathogenic
2749763	NM_004727.3(SLC24A1):c.1611del (p.Phe538fs)	Pathogenic
2986615	NM_004727.3(SLC24A1):c.152G>A (p.Trp51Ter)	Pathogenic
3250316	NM_004727.3(SLC24A1):c.41T>G (p.Leu14Ter)	Pathogenic
3359131	NM_004727.3(SLC24A1):c.642dup (p.Thr215fs)	Pathogenic
3700936	NM_004727.3(SLC24A1):c.2167dup (p.Val723fs)	Pathogenic
4717789	NM_004727.3(SLC24A1):c.28C>T (p.Gln10Ter)	Pathogenic
4736964	NM_004727.3(SLC24A1):c.2186_2187del (p.Pro729fs)	Pathogenic
4798469	NM_004727.3(SLC24A1):c.60del (p.His21fs)	Pathogenic
489397	NM_004727.3(SLC24A1):c.2401G>T (p.Glu801Ter)	Pathogenic
489399	NM_004727.3(SLC24A1):c.3291_3294del (p.Val1099fs)	Pathogenic
560509	NM_004727.3(SLC24A1):c.95T>A (p.Leu32Ter)	Pathogenic
954916	NM_004727.3(SLC24A1):c.823_824del (p.Val275fs)	Pathogenic

SpliceAI

1634 predictions. Top by Δscore:

Variant	Effect	Δscore
15:65622090:AAGG:A	donor_loss	0.9900
15:65622091:AGG:A	donor_loss	0.9900
15:65622092:GG:G	donor_loss	0.9900
15:65622093:G:GA	donor_loss	0.9900
15:65623953:AG:A	acceptor_gain	0.9900
15:65623954:GG:G	acceptor_gain	0.9900
15:65623954:GGGTT:G	acceptor_gain	0.9900
15:65638126:AGCC:A	acceptor_gain	0.9900
15:65638127:GCCG:G	acceptor_gain	0.9900
15:65639704:GT:G	donor_loss	0.9900
15:65639705:T:A	donor_loss	0.9900
15:65644425:A:AG	acceptor_gain	0.9900
15:65644426:G:GG	acceptor_gain	0.9900
15:65645610:A:G	acceptor_gain	0.9900
15:65645611:G:GG	acceptor_gain	0.9900
15:65650373:G:A	acceptor_gain	0.9900
15:65650376:TTGCA:T	acceptor_loss	0.9900
15:65650377:TGCA:T	acceptor_loss	0.9900
15:65650378:GCAGG:G	acceptor_loss	0.9900
15:65650379:CA:C	acceptor_loss	0.9900
15:65650380:A:AG	acceptor_gain	0.9900
15:65650381:G:GG	acceptor_gain	0.9900
15:65650381:G:GT	acceptor_loss	0.9900
15:65650381:GGAA:G	acceptor_gain	0.9900
15:65650940:CAGG:C	donor_loss	0.9900
15:65650943:GT:G	donor_loss	0.9900
15:65650944:T:G	donor_loss	0.9900
15:65653828:A:AG	acceptor_gain	0.9900
15:65653829:G:GG	acceptor_gain	0.9900
15:65653829:GCTT:G	acceptor_gain	0.9900

AlphaMissense

7246 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:65625668:G:C	G530R	1.000
15:65652718:T:C	L987P	1.000
15:65625585:C:A	A502D	0.999
15:65625600:C:A	P507H	0.999
15:65625606:T:C	L509P	0.999
15:65625663:T:A	I528N	0.999
15:65625668:G:T	G530C	0.999
15:65625669:G:A	G530D	0.999
15:65625669:G:T	G530V	0.999
15:65625675:C:A	A532D	0.999
15:65625680:T:C	F534L	0.999
15:65625682:C:A	F534L	0.999
15:65625682:C:G	F534L	0.999
15:65625685:C:A	N535K	0.999
15:65625685:C:G	N535K	0.999
15:65625701:G:C	G541R	0.999
15:65625702:G:A	G541D	0.999
15:65625786:T:C	L569P	0.999
15:65652678:G:C	G974R	0.999
15:65652682:T:C	L975P	0.999
15:65652691:T:A	L978H	0.999
15:65652691:T:C	L978P	0.999
15:65652726:A:C	S990R	0.999
15:65652728:T:A	S990R	0.999
15:65652728:T:G	S990R	0.999
15:65652736:T:A	V993D	0.999
15:65652763:C:A	A1002D	0.999
15:65652780:G:C	G1008R	0.999
15:65652781:G:A	G1008D	0.999
15:65652788:C:A	N1010K	0.999

dbSNP variants (sampled 300 via entrez): RS1000146171 (15:65637087 G>A), RS1000153911 (15:65651188 A>G,T), RS1000271900 (15:65623544 A>G), RS1000304699 (15:65609984 T>A), RS1000374292 (15:65630573 T>A,C), RS1000388149 (15:65610530 G>A), RS1000405018 (15:65616506 T>A), RS1000405541 (15:65630948 G>A), RS1000438443 (15:65651484 A>G,T), RS1000567995 (15:65617014 G>A,C), RS1000607605 (15:65625016 G>A), RS1000619051 (15:65610114 C>T), RS1000747548 (15:65618072 A>G), RS1000852880 (15:65649890 A>C,G), RS1000876205 (15:65611370 G>C)

Disease associations

OMIM: gene MIM:603617 | disease phenotypes: MIM:613830, MIM:163500, MIM:268000

GenCC curated gene-disease

Disease	Classification	Inheritance
congenital stationary night blindness 1D	Strong	Autosomal recessive
congenital stationary night blindness	Supportive	Autosomal dominant

ClinGen Gene-Disease Validity (1)

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

Disease	Classification	Inheritance
inherited retinal dystrophy	Definitive	AR

Mondo (6): congenital stationary night blindness 1D (MONDO:0013450), inherited retinal dystrophy (MONDO:0019118), optic atrophy (MONDO:0003608), congenital stationary night blindness autosomal dominant 2 (MONDO:0008099), retinitis pigmentosa (MONDO:0019200), congenital stationary night blindness (MONDO:0016293)

Orphanet (4): Congenital stationary night blindness (Orphanet:215), OBSOLETE: Inherited retinal disorder (Orphanet:71862), Retinitis pigmentosa (Orphanet:791), Moyamoya angiopathy (Orphanet:477768)

HPO phenotypes

6 total (7 of 6 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000580	Pigmentary retinopathy
HP:0007401	Macular atrophy
HP:0007642	Early-onset non-progressive night blindness
HP:0007843	Attenuation of retinal blood vessels
HP:0011463	Childhood onset
HP:0000556	Retinal dystrophy

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST000587_7	Mean corpuscular hemoglobin	3.000000e-09
GCST007006_14	Logical memory (delayed recall) in normal cognition	8.000000e-07
GCST010083_124	Hemoglobin levels	3.000000e-11
GCST011369_38	Iron status biomarkers (ferritin levels)	3.000000e-08

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004509	hemoglobin measurement
EFO:0004527	mean corpuscular hemoglobin
EFO:0004874	memory performance
EFO:0004459	ferritin measurement

MeSH disease descriptors (5)

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
C566869	Night Blindness, Congenital Stationary, Autosomal Dominant 2 (supp.)
C536122	Night blindness, congenital stationary (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — SLC24 family of sodium/potassium/calcium exchangers

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	3
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	increases abundance, affects cotreatment, increases expression	1
titanium dioxide	increases expression	1
butyraldehyde	decreases expression	1
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	1
pentanal	decreases expression	1
ICG 001	increases expression	1
abrine	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Acetaminophen	decreases expression	1
Acrolein	affects cotreatment, increases expression, increases abundance	1
Air Pollutants	increases expression, affects cotreatment, increases abundance	1
Cisplatin	decreases expression	1
Doxorubicin	decreases expression	1
Ozone	increases abundance, affects cotreatment, increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Silicon Dioxide	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Aflatoxin B1	increases methylation	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1
Volatile Organic Compounds	affects cotreatment, increases expression	1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D4J7	HCT116-SLC24A1-KO-c1	Cancer cell line	Male
CVCL_D4J8	HCT116-SLC24A1-KO-c5	Cancer cell line	Male
CVCL_TM02	HAP1 SLC24A1 (-) 1	Cancer cell line	Male
CVCL_XT00	HAP1 SLC24A1 (-) 2	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
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
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
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
NCT07290530	PHASE3	NOT_YET_RECRUITING	24-Month Trial of NPI-001 for the Preservation of Photoreceptors in Retinitis Pigmentosa Associated With Usher Syndrome
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]
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
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
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)
NCT05902962	PHASE1	COMPLETED	SAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects
NCT06319872	PHASE1	RECRUITING	The Effects of Disulfiram (Antabuse®) on Visual Acuity in Patients With Retinal Degeneration
NCT06455826	PHASE1	COMPLETED	MAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects (Wallaby)