SLC24A1 (solute carrier family 24 member 1)

Gene

• Entrez ID: 9187
• Gene name: Solute carrier family 24 member 1
• Gene symbol: SLC24A1
• Synonyms (NCBI Gene): CSNB1D, HsT17412, NCKX, NCKX1, RODX
• Chromosome: 15
• Chromosome location: 15q22.31
• Summary: 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

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs766780281	ATCT>-	Pathogenic	Intron variant, genic downstream transcript variant, frameshift variant, coding sequence variant
rs777989874	AT>-	Pathogenic	Coding sequence variant, frameshift variant, genic upstream transcript variant
rs1410075831	G>T	Pathogenic	Genic downstream transcript variant, coding sequence variant, downstream transcript variant, stop gained
rs1555403793	TCT>-	Pathogenic	Inframe deletion, coding sequence variant, genic upstream transcript variant
rs1555407654	A>C	Pathogenic	Genic downstream transcript variant, missense variant, coding sequence variant, intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1354757	hsa-miR-15a	CLIP-seq
MIRT1354758	hsa-miR-15b	CLIP-seq
MIRT1354759	hsa-miR-16	CLIP-seq
MIRT1354760	hsa-miR-195	CLIP-seq
MIRT1354761	hsa-miR-2116	CLIP-seq
MIRT1354762	hsa-miR-3122	CLIP-seq
MIRT1354763	hsa-miR-3145-3p	CLIP-seq
MIRT1354764	hsa-miR-3157-5p	CLIP-seq
MIRT1354765	hsa-miR-3201	CLIP-seq
MIRT1354766	hsa-miR-325	CLIP-seq
MIRT1354767	hsa-miR-340	CLIP-seq
MIRT1354768	hsa-miR-3681	CLIP-seq
MIRT1354769	hsa-miR-3689a-3p	CLIP-seq
MIRT1354770	hsa-miR-3689c	CLIP-seq
MIRT1354771	hsa-miR-3689d	CLIP-seq
MIRT1354772	hsa-miR-3913-5p	CLIP-seq
MIRT1354773	hsa-miR-424	CLIP-seq
MIRT1354774	hsa-miR-4276	CLIP-seq
MIRT1354775	hsa-miR-4279	CLIP-seq
MIRT1354776	hsa-miR-4297	CLIP-seq
MIRT1354777	hsa-miR-4317	CLIP-seq
MIRT1354778	hsa-miR-4655-5p	CLIP-seq
MIRT1354779	hsa-miR-4677-5p	CLIP-seq
MIRT1354780	hsa-miR-4699-3p	CLIP-seq
MIRT1354781	hsa-miR-4728-5p	CLIP-seq
MIRT1354782	hsa-miR-4791	CLIP-seq
MIRT1354783	hsa-miR-493	CLIP-seq
MIRT1354784	hsa-miR-497	CLIP-seq
MIRT1354785	hsa-miR-550b	CLIP-seq
MIRT1354786	hsa-miR-576-3p	CLIP-seq
MIRT1354787	hsa-miR-587	CLIP-seq
MIRT1354788	hsa-miR-622	CLIP-seq
MIRT1354789	hsa-miR-628-3p	CLIP-seq
MIRT1354790	hsa-miR-942	CLIP-seq
MIRT2105073	hsa-miR-1273e	CLIP-seq
MIRT2105074	hsa-miR-1827	CLIP-seq
MIRT2105075	hsa-miR-2964a-3p	CLIP-seq
MIRT2105076	hsa-miR-302f	CLIP-seq
MIRT2105077	hsa-miR-3650	CLIP-seq
MIRT1354771	hsa-miR-3689d	CLIP-seq
MIRT2105078	hsa-miR-3942-3p	CLIP-seq
MIRT1354778	hsa-miR-4655-5p	CLIP-seq
MIRT2105079	hsa-miR-4722-5p	CLIP-seq
MIRT2105080	hsa-miR-4768-3p	CLIP-seq
MIRT2105081	hsa-miR-513a-3p	CLIP-seq
MIRT2105082	hsa-miR-940	CLIP-seq
MIRT2329654	hsa-miR-1262	CLIP-seq
MIRT2329655	hsa-miR-1283	CLIP-seq
MIRT2329656	hsa-miR-1287	CLIP-seq
MIRT2329657	hsa-miR-146a	CLIP-seq
MIRT2329658	hsa-miR-146b-5p	CLIP-seq
MIRT2329659	hsa-miR-188-3p	CLIP-seq
MIRT2329660	hsa-miR-2054	CLIP-seq
MIRT2329661	hsa-miR-3135b	CLIP-seq
MIRT2329662	hsa-miR-3147	CLIP-seq
MIRT2329663	hsa-miR-3929	CLIP-seq
MIRT2329664	hsa-miR-4289	CLIP-seq
MIRT2329665	hsa-miR-4417	CLIP-seq
MIRT2329666	hsa-miR-4419b	CLIP-seq
MIRT2329667	hsa-miR-4425	CLIP-seq
MIRT2329668	hsa-miR-4478	CLIP-seq
MIRT2329669	hsa-miR-4649-3p	CLIP-seq
MIRT2329670	hsa-miR-4701-3p	CLIP-seq
MIRT2329671	hsa-miR-589	CLIP-seq
MIRT2329672	hsa-miR-616	CLIP-seq
MIRT2329654	hsa-miR-1262	CLIP-seq
MIRT2329657	hsa-miR-146a	CLIP-seq
MIRT2329658	hsa-miR-146b-5p	CLIP-seq
MIRT2329662	hsa-miR-3147	CLIP-seq
MIRT2329664	hsa-miR-4289	CLIP-seq
MIRT2329667	hsa-miR-4425	CLIP-seq
MIRT2329670	hsa-miR-4701-3p	CLIP-seq
MIRT2329671	hsa-miR-589	CLIP-seq
MIRT2329672	hsa-miR-616	CLIP-seq
MIRT2329654	hsa-miR-1262	CLIP-seq
MIRT2329656	hsa-miR-1287	CLIP-seq
MIRT2329657	hsa-miR-146a	CLIP-seq
MIRT2329658	hsa-miR-146b-5p	CLIP-seq
MIRT2329660	hsa-miR-2054	CLIP-seq
MIRT1354762	hsa-miR-3122	CLIP-seq
MIRT2329661	hsa-miR-3135b	CLIP-seq
MIRT2329662	hsa-miR-3147	CLIP-seq
MIRT1354769	hsa-miR-3689a-3p	CLIP-seq
MIRT1354770	hsa-miR-3689c	CLIP-seq
MIRT1354772	hsa-miR-3913-5p	CLIP-seq
MIRT2329667	hsa-miR-4425	CLIP-seq
MIRT1354780	hsa-miR-4699-3p	CLIP-seq
MIRT2329670	hsa-miR-4701-3p	CLIP-seq
MIRT1354781	hsa-miR-4728-5p	CLIP-seq
MIRT2329671	hsa-miR-589	CLIP-seq
MIRT2623933	hsa-miR-200b	CLIP-seq
MIRT2623934	hsa-miR-200c	CLIP-seq
MIRT2623935	hsa-miR-3120-5p	CLIP-seq
MIRT2623936	hsa-miR-3613-3p	CLIP-seq
MIRT2623937	hsa-miR-3664-5p	CLIP-seq
MIRT2623938	hsa-miR-371-5p	CLIP-seq
MIRT2623939	hsa-miR-371b-5p	CLIP-seq
MIRT2623940	hsa-miR-429	CLIP-seq
MIRT2623933	hsa-miR-200b	CLIP-seq
MIRT2623934	hsa-miR-200c	CLIP-seq
MIRT2623935	hsa-miR-3120-5p	CLIP-seq
MIRT2623936	hsa-miR-3613-3p	CLIP-seq
MIRT2623937	hsa-miR-3664-5p	CLIP-seq
MIRT2623938	hsa-miR-371-5p	CLIP-seq
MIRT2623939	hsa-miR-371b-5p	CLIP-seq
MIRT2623940	hsa-miR-429	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005262	Function	Calcium channel activity	IBA
GO:0005515	Function	Protein binding	IPI	17474147
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA	26631410
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	RCA	26631410
GO:0005886	Component	Plasma membrane	TAS	9478004
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006811	Process	Monoatomic ion transport	TAS
GO:0006816	Process	Calcium ion transport	IEA
GO:0006816	Process	Calcium ion transport	NAS	7539424
GO:0006874	Process	Intracellular calcium ion homeostasis	IBA
GO:0006874	Process	Intracellular calcium ion homeostasis	IDA	26631410
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	NAS	9856482
GO:0008273	Function	Calcium, potassium:sodium antiporter activity	IBA
GO:0008273	Function	Calcium, potassium:sodium antiporter activity	IDA	26631410
GO:0008273	Function	Calcium, potassium:sodium antiporter activity	IEA
GO:0008273	Function	Calcium, potassium:sodium antiporter activity	ISS	10662833
GO:0008273	Function	Calcium, potassium:sodium antiporter activity	NAS	9478004
GO:0008273	Function	Calcium, potassium:sodium antiporter activity	TAS
GO:0009642	Process	Response to light intensity	NAS	9856482
GO:0015293	Function	Symporter activity	IEA
GO:0015297	Function	Antiporter activity	IEA
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	9478004
GO:0019867	Component	Outer membrane	NAS	9856482
GO:0035725	Process	Sodium ion transmembrane transport	IDA	26631410
GO:0043025	Component	Neuronal cell body	ISS	10662833
GO:0055085	Process	Transmembrane transport	IEA
GO:0060291	Process	Long-term synaptic potentiation	IBA
GO:0060292	Process	Long-term synaptic depression	IBA
GO:0070588	Process	Calcium ion transmembrane transport	IBA
GO:0070588	Process	Calcium ion transmembrane transport	IDA	26631410
GO:0071805	Process	Potassium ion transmembrane transport	IDA	26631410
GO:0098703	Process	Calcium ion import across plasma membrane	ISS	10662833

Other IDs

• MIM: 603617
• HGNC: 10975
• e!Ensembl: ENSG00000074621

Protein

• UniProt ID: O60721
• Protein name: Sodium/potassium/calcium exchanger 1 (Na(+)/K(+)/Ca(2+)-exchange protein 1) (Retinal rod Na-Ca+K exchanger) (Solute carrier family 24 member 1)
• Protein function: Calcium, potassium:sodium antiporter that transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+) (PubMed:26631410). Critical component of the visual transduction cascade, controlling the calcium concentration of outer segments during light and d
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01699	Na_Ca_ex	458 → 602	Sodium/calcium exchanger protein	Family
  PF01699	Na_Ca_ex	936 → 1087	Sodium/calcium exchanger protein	Family

• Tissue specificity: TISSUE SPECIFICITY: Expressed in the retina, particularly in the inner segment, outer and inner nuclear layers, and ganglion cell layer. {ECO:0000269|PubMed:20850105}.
• Sequence:

  MGKLIRMGPQERWLLRTKRLHWSRLLFLLGMLIIGSTYQHLRRPRGLSSLWAAVSSHQPI
  KLASRDLSSEEMMMMSSSPSKPSSEMGGKMLVPQASVGSDEATLSMTVENIPSMPKRTAK
  MIPTTTKNNYSPTAAGTERRKEDTPTSSRTLTYYTSTSSRQIVKKYTPTPRGEMKSYSPT
  QVREKVKYTPSPRGRRVGTYVPSTFMTMETSHAITPRTTVKDSDITATYKILETNSLKRI
  MEETTPTTLKGMFDSTPTFLTHEVEANVLTSPRSVMEKNNLFPPRRVESNSSAHPWGLVG
  KSNPKTPQGTVLLHTPATSEGQVTISTMTGSSPAETKAFTAAWSLRNPSPRTSVSAIKTA
  PAIVWRLAKKPSTAPSTSTTPTVRAKLTMQVHHCVVVKPTPAMLTTPSPSLTTALLPEEL
  SPSPSVLPPSLPDLHPKGEYPPDLFSVEERRQGWVVLHVFGMMYVFVALAIVCDEYFVPA
  LGVITDKLQISEDVAGATFMAAGGSAPELFTSLIGVFISHSNVGIGTIVGSAVFNILFVI
  GTCSLFSREILNLTWWPLFRDVSFYILDLIMLILFFLDSLIAWWESLLLLLAYAFYVFTM
  KWNKHIEVWVKEQLSRRPVAKVMALEDLSKPGDGAIAVDELQDNKKLKLPSLLTRGSSST
  SLHNSTIRSTIYQLMLHSLDPLREVRLAKEKEEESLNQGARAQPQAKAESKPEEEEPAKL
  PAVTVTPAPVPDIKGDQKENPGGQEDVAEAESTGEMPGEEGETAGEGETEEKSGGETQPE
  GEGETETQGKGEECEDENEAEGKGDNEGEDEGEIHAEDGEMKGNEGETESQELSAENHGE
  AKNDEKGVEDGGGSDGGDSEEEEEEEEEQEEEEEEEEQEEEEEEEEEEEEKGNEEPLSLD
  WPETRQKQAIYLFLLPIVFPLWLTVPDVRRQESRKFFVFTFLGSIMWIAMFSYLMVWWAH
  QVGETIGISEEIMGLTILAAGTSIPDLITSVIVARKGLGDMAVSSSVGSNIFDITVGLPV
  PWLLFSLINGLQPVPVSSNGLFCAIVLLFLMLLFVISSIASCKWRMNKILGFTMFLLYFV
  FLIISVMLEDRIISCPVSV

• Sequence length: 1099

Pathways

KEGG:

Phototransduction

Reactome:

Sodium/Calcium exchangers
Defective SLC24A1 causes congenital stationary night blindness 1D (CSNB1D)

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Colorectal cancer	Likely pathogenic	rs766014688	RCV005922636	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital stationary night blindness 1D	Pathogenic; Likely pathogenic	rs201452975, rs766014688, rs762665302, rs767508005, rs1410075831, rs766780281, rs1566945534, rs777989874	RCV002488199 RCV001807971 RCV005631252 RCV000023321 RCV000579382 RCV000579381 RCV005253062 RCV000989346	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Congenital stationary night blindness autosomal dominant 2	Likely pathogenic; Pathogenic	rs777989874	RCV004760695	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Malignant tumor of urinary bladder	Pathogenic	rs748399766	RCV005924374	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Moyamoya angiopathy	Likely pathogenic	rs2074441517	RCV004704495	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Likely pathogenic; Pathogenic	rs777989874, rs200047855, rs2074443699, rs1566947860	RCV001074186 RCV001073408 RCV001073405 RCV001074383	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis pigmentosa	Pathogenic; Likely pathogenic	rs1566945534, rs777989874	RCV000678630 RCV000678629	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SLC24A1-related disorder	Pathogenic; Likely pathogenic	rs201452975, rs777989874	RCV004754746 RCV003411588	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL STATIONARY NIGHT BLINDNESS	—	GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Stationary Night Blindness, Recessive	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NIGHT BLINDNESS, CONGENITAL STATIONARY	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NIGHT BLINDNESS, CONGENITAL STATIONARY, AUTOSOMAL DOMINANT 2	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 1D	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OGUCHI DISEASE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OPTIC ATROPHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Cone-rod synaptic disorder, congenital nonprogressive	Congenital stationary night blindness	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Congenital stationary night blindness	Congenital stationary night blindness	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Disorder of eye	Disorder Of Eye	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Hypoplasia of optic disc	Hypoplasia Of Optic Disc	HPO_DG			★☆☆☆☆ Found in Text Mining only
Myofibrillar Myopathy	Myofibrillar myopathy	BEFREE	30289745		★☆☆☆☆ Found in Text Mining only
Night blindness congenital stationary	Night blindness, congenital stationary	Pubtator	35486108	Associate	★☆☆☆☆ Found in Text Mining only
Night blindness, congenital stationary	Night blindness	BEFREE	20850105, 26822852		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Night blindness, congenital stationary	Night blindness	ORPHANET_DG	20850105		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Night blindness, congenital stationary	Night blindness	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Night blindness, congenital stationary	Night blindness	GENOMICS_ENGLAND_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Night blindness, congenital stationary	Night blindness	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Night blindness, congenital stationary, type 1	Night blindness	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Night Blindness, Congenital Stationary, Type 1A	Night blindness	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 1B	Night blindness	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 1D	Night blindness	GENOMICS_ENGLAND_DG	20850105		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 1D	Night blindness	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 2A	Night blindness	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 2B (disorder)	Night blindness	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Nyctalopia	Nyctalopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal Diseases	BEFREE	27624628		★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	27624628		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis pigmentosa	Pubtator	27624628, 35486108	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis Pigmentosa	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Seizures	Seizures	Pubtator	27129268	Associate	★☆☆☆☆ Found in Text Mining only
Severe myopia	Myopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only
X-Linked Csnb	Congenital stationary night blindness, X-Linked	CTD_human_DG			★☆☆☆☆ Found in Text Mining only