Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	9187
Gene name	Solute carrier family 24 member 1
Gene symbol	SLC24A1
Synonyms (NCBI Gene)	CSNB1DHsT17412NCKXNCKX1RODX
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

Show/Hide all (5)

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

106

Show/Hide all (106)

miRTarBase ID	miRNA	Experiments
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

Show/Hide all (36)

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

MIM	HGNC	e!Ensembl
603617	10975	ENSG00000074621

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

Interactions

View interactions

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

166

Show/Hide Causal Diseases (8)

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

Show/Hide Unknown Diseases (10)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cholangiocarcinoma	Benign	rs3743171	RCV005892747
Colon adenocarcinoma	Benign	rs35571449, rs35366838	RCV005892748 RCV005893407
Congenital Stationary Night Blindness, Recessive	Uncertain significance	rs886051355, rs371550495	RCV000302986 RCV000306662
Familial cancer of breast	Likely benign	rs188449742	RCV005926144
Gastric cancer	Benign	rs200712030	RCV005914151
Sarcoma	Benign	rs35366838	RCV005893408
Thymoma	Benign	rs35571449	RCV005892750
Thyroid cancer, nonmedullary, 1	Likely benign	rs567874420	RCV005925404
Uterine corpus endometrial carcinoma	Uncertain significance	rs375544210	RCV005911062
Uveal melanoma	Benign	rs35571449	RCV005892749

Show/Hide Text Mining Associations (4)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Night blindness congenital stationary	Associate	35486108
Pigmentation Disorders	Associate	27129268
Retinitis Pigmentosa	Associate	27624628, 35486108
Seizures	Associate	27129268

SLC24A1 (solute carrier family 24 member 1)