SLC24A1 solute carrier family 24 member 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC24A1provided by HGNC
Official Full Name: solute carrier family 24 member 1provided by HGNC
Primary source: HGNC:HGNC:10975
See related: Ensembl:ENSG00000074621 MIM:603617; AllianceGenome:HGNC:10975
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NCKX; RODX; NCKX1; CSNB1D; HsT17412
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 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. [provided by RefSeq, Dec 2011]
Expression: Ubiquitous expression in thyroid (RPKM 3.0), testis (RPKM 2.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q22.31

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (65611350..65661002)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (63420643..63470640)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (65903688..65953340)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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
Title: Panel-Based Population Next-Generation Sequencing for Inherited Retinal Degenerations.
The index patient and his affected brother carry a homozygous single-nucleotide variants (SNVs) in sodium-calcium, potassium exchanger (SLC24A1) (c.2401G > T).
Title: Next-generation sequencing confirms the implication of SLC24A1 in autosomal-recessive congenital stationary night blindness.
A mutation in SLC24A1 is implicated in autosomal-recessive congenital stationary night blindness.
Title: A mutation in SLC24A1 implicated in autosomal-recessive congenital stationary night blindness.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Congenital stationary night blindness 1D MedGen: C3151193 OMIM: 613830 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study of hematological and biochemical traits in a Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of solute carrier family 24 (sodium/potassium/calcium exchanger), member 1 (SLC24A1) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
capsid	gag	The interaction of HIV-1 CA with human cellular solute carrier family 24, member 1 protein (SLC24A1) is identified by yeast two-hybrid screen	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G32806 (e-PCR)
- UniSTS:117385

A009S19 (e-PCR)
- UniSTS:3509

SLC24A1_1761.2 (e-PCR)
- UniSTS:281013

PMC150727P6 (e-PCR)
- UniSTS:271095

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables calcium, potassium:sodium antiporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables calcium, potassium:sodium antiporter activity	IDA Inferred from Direct Assay more info	PubMed
enables calcium, potassium:sodium antiporter activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables calcium, potassium:sodium antiporter activity	NAS Non-traceable Author Statement more info	PubMed
enables calcium, potassium:sodium antiporter activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables symporter activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in calcium ion import across plasma membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in calcium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in calcium ion transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in calcium ion transport	NAS Non-traceable Author Statement more info	PubMed
involved_in intracellular calcium ion homeostasis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within intracellular calcium ion homeostasis	IDA Inferred from Direct Assay more info	PubMed
involved_in long-term synaptic depression	IBA Inferred from Biological aspect of Ancestor more info
involved_in long-term synaptic potentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in monoatomic ion transport	TAS Traceable Author Statement more info
involved_in potassium ion transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in response to light intensity	NAS Non-traceable Author Statement more info	PubMed
involved_in sodium ion transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in visual perception	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cell surface	IEA Inferred from Electronic Annotation more info
located_in membrane	TAS Traceable Author Statement more info	PubMed
located_in neuronal cell body	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in outer membrane	NAS Non-traceable Author Statement more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	RCA inferred from Reviewed Computational Analysis more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: sodium/potassium/calcium exchanger 1

Names: Na(+)/K(+)/Ca(2+)-exchange protein 1; Na/Ca-K exchanger 1; retinal rod Na+/Ca+/K+ exchanger; solute carrier family 24 (sodium/potassium/calcium exchanger), member 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_031968.2 RefSeqGene

Range

15534..49856

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001254740.2 → NP_001241669.1 sodium/potassium/calcium exchanger 1 isoform 2

See identical proteins and their annotated locations for NP_001241669.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.

Source sequence(s)

AC011939, AC027220, AK300633

UniProtKB/TrEMBL

B4DUG1

Conserved Domains (1) summary

pfam01699
Location:263 → 414

Na_Ca_ex; Sodium/calcium exchanger protein
NM_001301031.1 → NP_001287960.1 sodium/potassium/calcium exchanger 1 isoform 3

See identical proteins and their annotated locations for NP_001287960.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.

Source sequence(s)

AI026072, AK304006, BC117263, BM129630, BM681488, EL947516, EL948740

Consensus CDS

CCDS73742.1

UniProtKB/TrEMBL

B4E1W0

Related

ENSP00000381991.4, ENST00000399033.8

Conserved Domains (2) summary

TIGR00927
Location:1 → 1069

2A1904; K+-dependent Na+/Ca+ exchanger

pfam01699
Location:458 → 602

Na_Ca_ex; Sodium/calcium exchanger protein
NM_001301032.1 → NP_001287961.1 sodium/potassium/calcium exchanger 1 isoform 4

See identical proteins and their annotated locations for NP_001287961.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR, and lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.

Source sequence(s)

AB014602, AF026132, AI026072, BM129630, BM681488, EL947516, EL948740

Consensus CDS

CCDS73743.1

UniProtKB/TrEMBL

B4E1W0

Related

ENSP00000439190.1, ENST00000546330.1

Conserved Domains (2) summary

TIGR00927
Location:1 → 1081

2A1904; K+-dependent Na+/Ca+ exchanger

pfam01699
Location:458 → 602

Na_Ca_ex; Sodium/calcium exchanger protein
NM_001301033.2 → NP_001287962.1 sodium/potassium/calcium exchanger 1 isoform 5

See identical proteins and their annotated locations for NP_001287962.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR, lacks an alternate in-frame exon in the central coding region, and contains alternate 3' exon structure and thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (5) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AB014602, AC011939, AC027220, AK304006

Consensus CDS

CCDS73744.1

UniProtKB/TrEMBL

B4E1W0, F5H127

Related

ENSP00000439693.1, ENST00000537259.5

Conserved Domains (1) summary

cl27511
Location:1 → 1000

Na_Ca_ex; Sodium/calcium exchanger protein
NM_001411142.1 → NP_001398071.1 sodium/potassium/calcium exchanger 1 isoform 6

Status: REVIEWED

Source sequence(s)

AC011939, AC027220

Consensus CDS

CCDS92023.1

UniProtKB/TrEMBL

F5H483

Related

ENSP00000445163.1, ENST00000544319.6
NM_004727.3 → NP_004718.1 sodium/potassium/calcium exchanger 1 isoform 1

See identical proteins and their annotated locations for NP_004718.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC011939, AC027220, AF062922

Consensus CDS

CCDS45284.1

UniProtKB/Swiss-Prot

O43485, O60721, O75184, Q17RM9

UniProtKB/TrEMBL

B4E1W0

Related

ENSP00000261892.6, ENST00000261892.11

Conserved Domains (1) summary

TIGR00927
Location:1 → 1099

2A1904; K+-dependent Na+/Ca+ exchanger

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000015.10 Reference GRCh38.p14 Primary Assembly

Range

65611350..65661002

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024450103.2 → XP_024305871.1 sodium/potassium/calcium exchanger 1 isoform X1

UniProtKB/Swiss-Prot

O43485, O60721, O75184, Q17RM9

UniProtKB/TrEMBL

B4E1W0

Conserved Domains (1) summary

TIGR00927
Location:1 → 1099

2A1904; K+-dependent Na+/Ca+ exchanger
XM_011522219.2 → XP_011520521.1 sodium/potassium/calcium exchanger 1 isoform X1

See identical proteins and their annotated locations for XP_011520521.1

UniProtKB/Swiss-Prot

O43485, O60721, O75184, Q17RM9

UniProtKB/TrEMBL

B4E1W0

Conserved Domains (1) summary

TIGR00927
Location:1 → 1099

2A1904; K+-dependent Na+/Ca+ exchanger
XM_024450105.2 → XP_024305873.1 sodium/potassium/calcium exchanger 1 isoform X1

UniProtKB/Swiss-Prot

O43485, O60721, O75184, Q17RM9

UniProtKB/TrEMBL

B4E1W0

Conserved Domains (1) summary

TIGR00927
Location:1 → 1099

2A1904; K+-dependent Na+/Ca+ exchanger
XM_047433325.1 → XP_047289281.1 sodium/potassium/calcium exchanger 1 isoform X2
XM_024450104.2 → XP_024305872.1 sodium/potassium/calcium exchanger 1 isoform X1

UniProtKB/Swiss-Prot

O43485, O60721, O75184, Q17RM9

UniProtKB/TrEMBL

B4E1W0

Conserved Domains (1) summary

TIGR00927
Location:1 → 1099

2A1904; K+-dependent Na+/Ca+ exchanger
XM_047433326.1 → XP_047289282.1 sodium/potassium/calcium exchanger 1 isoform X2
XM_047433330.1 → XP_047289286.1 sodium/potassium/calcium exchanger 1 isoform X7
XM_011522222.4 → XP_011520524.1 sodium/potassium/calcium exchanger 1 isoform X7

See identical proteins and their annotated locations for XP_011520524.1

UniProtKB/TrEMBL

B4E1W0

Conserved Domains (2) summary

TIGR00927
Location:1 → 1018

2A1904; K+-dependent Na+/Ca+ exchanger

pfam01699
Location:458 → 602

Na_Ca_ex; Sodium/calcium exchanger protein
XM_047433333.1 → XP_047289289.1 sodium/potassium/calcium exchanger 1 isoform X10
XM_047433334.1 → XP_047289290.1 sodium/potassium/calcium exchanger 1 isoform X11
XM_047433338.1 → XP_047289294.1 sodium/potassium/calcium exchanger 1 isoform X15
XM_011522221.4 → XP_011520523.1 sodium/potassium/calcium exchanger 1 isoform X3

See identical proteins and their annotated locations for XP_011520523.1

UniProtKB/TrEMBL

B4E1W0

Conserved Domains (2) summary

TIGR00927
Location:1 → 1069

2A1904; K+-dependent Na+/Ca+ exchanger

pfam01699
Location:458 → 602

Na_Ca_ex; Sodium/calcium exchanger protein
XM_047433327.1 → XP_047289283.1 sodium/potassium/calcium exchanger 1 isoform X4
XM_047433335.1 → XP_047289291.1 sodium/potassium/calcium exchanger 1 isoform X13
XM_017022724.3 → XP_016878213.1 sodium/potassium/calcium exchanger 1 isoform X5

UniProtKB/TrEMBL

B4E1W0
XM_047433331.1 → XP_047289287.1 sodium/potassium/calcium exchanger 1 isoform X8
XM_017022725.3 → XP_016878214.1 sodium/potassium/calcium exchanger 1 isoform X12

UniProtKB/TrEMBL

B4E1W0
XM_047433328.1 → XP_047289284.1 sodium/potassium/calcium exchanger 1 isoform X6
XM_047433332.1 → XP_047289288.1 sodium/potassium/calcium exchanger 1 isoform X9
XM_047433336.1 → XP_047289292.1 sodium/potassium/calcium exchanger 1 isoform X14
XM_005254781.5 → XP_005254838.1 sodium/potassium/calcium exchanger 1 isoform X16

Conserved Domains (2) summary

TIGR00927
Location:1 → 637

2A1904; K+-dependent Na+/Ca+ exchanger

pfam01699
Location:458 → 602

Na_Ca_ex; Sodium/calcium exchanger protein
XM_011522226.4 → XP_011520528.1 sodium/potassium/calcium exchanger 1 isoform X17

Conserved Domains (2) summary

TIGR00927
Location:1 → 637

2A1904; K+-dependent Na+/Ca+ exchanger

pfam01699
Location:458 → 602

Na_Ca_ex; Sodium/calcium exchanger protein
XM_047433339.1 → XP_047289295.1 sodium/potassium/calcium exchanger 1 isoform X18

RNA

XR_007064494.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060939.1 Alternate T2T-CHM13v2.0

Range

63420643..63470640

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054379191.1 → XP_054235166.1 sodium/potassium/calcium exchanger 1 isoform X1

UniProtKB/Swiss-Prot

O43485, O60721, O75184, Q17RM9
XM_054379190.1 → XP_054235165.1 sodium/potassium/calcium exchanger 1 isoform X1

UniProtKB/Swiss-Prot

O43485, O60721, O75184, Q17RM9
XM_054379193.1 → XP_054235168.1 sodium/potassium/calcium exchanger 1 isoform X1

UniProtKB/Swiss-Prot

O43485, O60721, O75184, Q17RM9
XM_054379192.1 → XP_054235167.1 sodium/potassium/calcium exchanger 1 isoform X1

UniProtKB/Swiss-Prot

O43485, O60721, O75184, Q17RM9
XM_054379194.1 → XP_054235169.1 sodium/potassium/calcium exchanger 1 isoform X2
XM_054379195.1 → XP_054235170.1 sodium/potassium/calcium exchanger 1 isoform X2
XM_054379200.1 → XP_054235175.1 sodium/potassium/calcium exchanger 1 isoform X7
XM_054379201.1 → XP_054235176.1 sodium/potassium/calcium exchanger 1 isoform X7
XM_054379204.1 → XP_054235179.1 sodium/potassium/calcium exchanger 1 isoform X10
XM_054379205.1 → XP_054235180.1 sodium/potassium/calcium exchanger 1 isoform X11
XM_054379209.1 → XP_054235184.1 sodium/potassium/calcium exchanger 1 isoform X15
XM_054379198.1 → XP_054235173.1 sodium/potassium/calcium exchanger 1 isoform X5
XM_054379196.1 → XP_054235171.1 sodium/potassium/calcium exchanger 1 isoform X3
XM_054379202.1 → XP_054235177.1 sodium/potassium/calcium exchanger 1 isoform X8
XM_054379206.1 → XP_054235181.1 sodium/potassium/calcium exchanger 1 isoform X12
XM_054379199.1 → XP_054235174.1 sodium/potassium/calcium exchanger 1 isoform X6
XM_054379197.1 → XP_054235172.1 sodium/potassium/calcium exchanger 1 isoform X4
XM_054379203.1 → XP_054235178.1 sodium/potassium/calcium exchanger 1 isoform X9
XM_054379208.1 → XP_054235183.1 sodium/potassium/calcium exchanger 1 isoform X14
XM_054379207.1 → XP_054235182.1 sodium/potassium/calcium exchanger 1 isoform X13
XM_054379210.1 → XP_054235185.1 sodium/potassium/calcium exchanger 1 isoform X16
XM_054379211.1 → XP_054235186.1 sodium/potassium/calcium exchanger 1 isoform X17
XM_054379212.1 → XP_054235187.1 sodium/potassium/calcium exchanger 1 isoform X18