SLC24A3 (solute carrier family 24 member 3) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: SLC24A3 (solute carrier family 24 member 3) Homo sapiens
Analyze
Symbol: SLC24A3
Name: solute carrier family 24 member 3
RGD ID: 735914
HGNC Page HGNC:10977
Description: Enables calcium, potassium:sodium antiporter activity. Involved in calcium ion transmembrane transport; potassium ion transmembrane transport; and sodium ion transmembrane transport. Acts upstream of or within intracellular calcium ion homeostasis. Located in plasma membrane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Na(+)/K(+)/Ca(2+)-exchange protein 3; NCKX3; sodium calcium exchanger; sodium/potassium/calcium exchanger 3; solute carrier family 24 (sodium/potassium/calcium exchanger), member 3
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382019,212,642 - 19,722,926 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2019,212,642 - 19,722,926 (+)EnsemblGRCh38hg38GRCh38
GRCh372019,193,286 - 19,703,570 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362019,141,290 - 19,651,541 (+)NCBINCBI36Build 36hg18NCBI36
Build 342019,141,289 - 19,651,540NCBI
Celera2019,267,475 - 19,777,636 (+)NCBICelera
Cytogenetic Map20p11.23NCBI
HuRef2019,155,790 - 19,666,236 (+)NCBIHuRef
CHM1_12019,262,244 - 19,704,077 (+)NCBICHM1_1
T2T-CHM13v2.02019,264,159 - 19,774,968 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cell periphery  (IDA,IEA,ISS)
membrane  (IEA)
plasma membrane  (IBA,IDA,IEA,RCA,TAS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. Na+/Ca2+ exchangers: three mammalian gene families control Ca2+ transport. Lytton J Biochem J. 2007 Sep 15;406(3):365-82.
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11294880   PMID:11780052   PMID:20031604   PMID:20379614   PMID:21321244   PMID:21685187   PMID:21873635   PMID:22424883   PMID:24132900   PMID:26631410   PMID:30280653   PMID:33961781  


Genomics

Comparative Map Data
SLC24A3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382019,212,642 - 19,722,926 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2019,212,642 - 19,722,926 (+)EnsemblGRCh38hg38GRCh38
GRCh372019,193,286 - 19,703,570 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362019,141,290 - 19,651,541 (+)NCBINCBI36Build 36hg18NCBI36
Build 342019,141,289 - 19,651,540NCBI
Celera2019,267,475 - 19,777,636 (+)NCBICelera
Cytogenetic Map20p11.23NCBI
HuRef2019,155,790 - 19,666,236 (+)NCBIHuRef
CHM1_12019,262,244 - 19,704,077 (+)NCBICHM1_1
T2T-CHM13v2.02019,264,159 - 19,774,968 (+)NCBIT2T-CHM13v2.0
Slc24a3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392145,009,695 - 145,484,086 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2145,009,674 - 145,484,086 (+)EnsemblGRCm39 Ensembl
GRCm382145,167,775 - 145,642,166 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2145,167,754 - 145,642,166 (+)EnsemblGRCm38mm10GRCm38
MGSCv372145,068,347 - 145,467,689 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362144,934,052 - 145,333,394 (+)NCBIMGSCv36mm8
Celera2146,442,567 - 146,852,275 (+)NCBICelera
Cytogenetic Map2G1NCBI
cM Map271.08NCBI
Slc24a3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83153,005,418 - 153,504,497 (+)NCBIGRCr8
mRatBN7.23132,552,119 - 133,051,192 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3132,551,595 - 133,051,192 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3136,458,426 - 136,960,748 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03145,042,522 - 145,544,835 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03142,745,677 - 143,247,999 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03139,333,942 - 139,835,728 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3139,695,028 - 139,833,967 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03145,760,074 - 146,259,491 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43133,734,890 - 134,249,326 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13133,640,575 - 134,153,200 (+)NCBI
Celera3131,419,773 - 131,916,131 (+)NCBICelera
Cytogenetic Map3q41NCBI
Slc24a3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541527,477,819 - 27,928,383 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541527,477,801 - 27,930,108 (+)NCBIChiLan1.0ChiLan1.0
SLC24A3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22120,097,895 - 20,610,669 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12020,094,738 - 20,607,505 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02019,168,820 - 19,680,706 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12019,137,943 - 19,648,235 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2019,137,938 - 19,646,475 (+)Ensemblpanpan1.1panPan2
SLC24A3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1243,593,562 - 4,014,366 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl243,593,513 - 3,784,467 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha243,620,103 - 3,818,880 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0244,000,491 - 4,482,100 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl244,000,493 - 4,482,430 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1243,595,752 - 4,077,406 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0243,699,250 - 4,181,348 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0243,977,410 - 4,458,938 (-)NCBIUU_Cfam_GSD_1.0
Slc24a3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640152,206,337 - 152,654,468 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936485639,532 - 1,085,830 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936485637,715 - 1,085,860 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC24A3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1727,270,093 - 27,780,526 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11727,270,232 - 27,780,535 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21731,405,580 - 31,468,072 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC24A3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1248,238,872 - 48,736,517 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660783,017,793 - 3,516,931 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc24a3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474119,808,255 - 20,297,056 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474119,808,186 - 20,298,772 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SLC24A3
70 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 20p13-11.21(chr20:89939-25697564)x3 copy number gain See cases [RCV000051227] Chr20:89939..25697564 [GRCh38]
Chr20:70580..25678200 [GRCh37]
Chr20:18580..25626200 [NCBI36]
Chr20:20p13-11.21		 pathogenic
GRCh38/hg38 20p13-11.22(chr20:89939-21787252)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052996]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052996]|See cases [RCV000052996] Chr20:89939..21787252 [GRCh38]
Chr20:70580..21767890 [GRCh37]
Chr20:18580..21715890 [NCBI36]
Chr20:20p13-11.22		 pathogenic
GRCh38/hg38 20p12.2-q12(chr20:9811433-39316956)x3 copy number gain See cases [RCV000052999] Chr20:9811433..39316956 [GRCh38]
Chr20:9792081..37945599 [GRCh37]
Chr20:9740081..37379013 [NCBI36]
Chr20:20p12.2-q12		 pathogenic
NM_020689.3(SLC24A3):c.142+5639T>C single nucleotide variant Lung cancer [RCV000101448] Chr20:19218623 [GRCh38]
Chr20:19199267 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.3(SLC24A3):c.271+87796A>T single nucleotide variant Lung cancer [RCV000101449] Chr20:19368883 [GRCh38]
Chr20:19349527 [GRCh37]
Chr20:20p11.23		 uncertain significance
GRCh38/hg38 20p13-q11.1(chr20:80106-30227427)x3 copy number gain See cases [RCV000133996] Chr20:80106..30227427 [GRCh38]
Chr20:60747..29462103 [GRCh37]
Chr20:8747..28075764 [NCBI36]
Chr20:20p13-q11.1		 pathogenic
GRCh38/hg38 20p13-q13.33(chr20:99557-64277321)x3 copy number gain See cases [RCV000135859] Chr20:99557..64277321 [GRCh38]
Chr20:80198..62908674 [GRCh37]
Chr20:28198..62379118 [NCBI36]
Chr20:20p13-q13.33		 pathogenic
GRCh38/hg38 20p12.1-11.22(chr20:17772771-21426789)x1 copy number loss See cases [RCV000135439] Chr20:17772771..21426789 [GRCh38]
Chr20:17753416..21407427 [GRCh37]
Chr20:17701416..21355427 [NCBI36]
Chr20:20p12.1-11.22		 pathogenic
GRCh38/hg38 20p13-11.1(chr20:80927-26324843)x3 copy number gain See cases [RCV000142017] Chr20:80927..26324843 [GRCh38]
Chr20:61568..26305479 [GRCh37]
Chr20:9568..26253479 [NCBI36]
Chr20:20p13-11.1		 pathogenic
GRCh37/hg19 20p11.23(chr20:19662569-20003113)x3 copy number gain Breast ductal adenocarcinoma [RCV000207286] Chr20:19662569..20003113 [GRCh37]
Chr20:20p11.23		 uncertain significance
GRCh37/hg19 20p13-11.1(chr20:80198-26075841)x3 copy number gain See cases [RCV000239954] Chr20:80198..26075841 [GRCh37]
Chr20:20p13-11.1		 pathogenic
GRCh37/hg19 20p12.1-q11.21(chr20:17705775-31600738)x3 copy number gain See cases [RCV000240436] Chr20:17705775..31600738 [GRCh37]
Chr20:20p12.1-q11.21		 pathogenic
GRCh37/hg19 20p13-q11.21(chr20:80198-26208081)x3 copy number gain not provided [RCV000487461] Chr20:80198..26208081 [GRCh37]
Chr20:20p13-q11.21		 pathogenic
GRCh37/hg19 20p11.23-11.1(chr20:18500917-25847320)x1 copy number loss See cases [RCV000510621] Chr20:18500917..25847320 [GRCh37]
Chr20:20p11.23-11.1		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:61569-62915555)x3 copy number gain See cases [RCV000510832] Chr20:61569..62915555 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
NM_020689.4(SLC24A3):c.765G>A (p.Met255Ile) single nucleotide variant Inborn genetic diseases [RCV003262625] Chr20:19673652 [GRCh38]
Chr20:19654296 [GRCh37]
Chr20:20p11.23		 uncertain significance
GRCh37/hg19 20p13-q13.33(chr20:61569-62915555) copy number gain See cases [RCV000512450] Chr20:61569..62915555 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
Single allele duplication not provided [RCV000677978] Chr20:17705775..31600738 [GRCh37]
Chr20:20p12.1-q11.21		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62948788)x3 copy number gain not provided [RCV000741058] Chr20:63244..62948788 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62961294)x3 copy number gain not provided [RCV000741059] Chr20:63244..62961294 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62912463)x3 copy number gain not provided [RCV000741057] Chr20:63244..62912463 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
NM_020689.4(SLC24A3):c.80T>C (p.Leu27Pro) single nucleotide variant Inborn genetic diseases [RCV003245702] Chr20:19212922 [GRCh38]
Chr20:19193566 [GRCh37]
Chr20:20p11.23		 uncertain significance
GRCh37/hg19 20p12.3-11.22(chr20:8571696-22088650)x1 copy number loss not provided [RCV001007080] Chr20:8571696..22088650 [GRCh37]
Chr20:20p12.3-11.22		 pathogenic
NM_020689.4(SLC24A3):c.1027C>T (p.Arg343Trp) single nucleotide variant Inborn genetic diseases [RCV003266523] Chr20:19684301 [GRCh38]
Chr20:19664945 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.814G>T (p.Ala272Ser) single nucleotide variant Inborn genetic diseases [RCV003271669] Chr20:19681904 [GRCh38]
Chr20:19662548 [GRCh37]
Chr20:20p11.23		 uncertain significance
GRCh37/hg19 20p12.2-11.23(chr20:11716825-19331055) copy number gain not provided [RCV000767743] Chr20:11716825..19331055 [GRCh37]
Chr20:20p12.2-11.23		 pathogenic
NM_020689.4(SLC24A3):c.666G>C (p.Leu222=) single nucleotide variant not provided [RCV000927621] Chr20:19654115 [GRCh38]
Chr20:19634759 [GRCh37]
Chr20:20p11.23		 likely benign
NM_020689.4(SLC24A3):c.1719C>T (p.Tyr573=) single nucleotide variant not provided [RCV000911238] Chr20:19698680 [GRCh38]
Chr20:19679324 [GRCh37]
Chr20:20p11.23		 benign
GRCh37/hg19 20p13-11.1(chr20:61568-26305479)x3 copy number gain not provided [RCV001007068] Chr20:61568..26305479 [GRCh37]
Chr20:20p13-11.1		 pathogenic
GRCh37/hg19 20p11.23(chr20:19188940-19354118)x3 copy number gain not provided [RCV001795842] Chr20:19188940..19354118 [GRCh37]
Chr20:20p11.23		 uncertain significance
GRCh37/hg19 20p11.23-11.22(chr20:19292925-22187397) copy number loss not specified [RCV002052705] Chr20:19292925..22187397 [GRCh37]
Chr20:20p11.23-11.22		 pathogenic
GRCh37/hg19 20p11.23-q11.22(chr20:18665879-33903216)x3 copy number gain not provided [RCV001829151] Chr20:18665879..33903216 [GRCh37]
Chr20:20p11.23-q11.22		 likely pathogenic
NM_020689.4(SLC24A3):c.255G>C (p.Lys85Asn) single nucleotide variant Inborn genetic diseases [RCV002687436] Chr20:19281071 [GRCh38]
Chr20:19261715 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.44G>A (p.Arg15His) single nucleotide variant Inborn genetic diseases [RCV002777416] Chr20:19212886 [GRCh38]
Chr20:19193530 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.538G>C (p.Val180Leu) single nucleotide variant Inborn genetic diseases [RCV002692664] Chr20:19585470 [GRCh38]
Chr20:19566114 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.233A>C (p.Asp78Ala) single nucleotide variant Inborn genetic diseases [RCV002870028] Chr20:19281049 [GRCh38]
Chr20:19261693 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.8C>T (p.Pro3Leu) single nucleotide variant Inborn genetic diseases [RCV002848757] Chr20:19212850 [GRCh38]
Chr20:19193494 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.278A>T (p.His93Leu) single nucleotide variant Inborn genetic diseases [RCV002744024] Chr20:19515494 [GRCh38]
Chr20:19496138 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.1033T>C (p.Ser345Pro) single nucleotide variant Inborn genetic diseases [RCV002916306] Chr20:19684307 [GRCh38]
Chr20:19664951 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.1924G>C (p.Gly642Arg) single nucleotide variant Inborn genetic diseases [RCV002915377] Chr20:19721129 [GRCh38]
Chr20:19701773 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.17A>C (p.Asp6Ala) single nucleotide variant Inborn genetic diseases [RCV002718481] Chr20:19212859 [GRCh38]
Chr20:19193503 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.1213G>A (p.Ala405Thr) single nucleotide variant Inborn genetic diseases [RCV002675295] Chr20:19685250 [GRCh38]
Chr20:19665894 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.229G>A (p.Glu77Lys) single nucleotide variant Inborn genetic diseases [RCV002670384] Chr20:19281045 [GRCh38]
Chr20:19261689 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.29C>T (p.Ala10Val) single nucleotide variant Inborn genetic diseases [RCV002965279] Chr20:19212871 [GRCh38]
Chr20:19193515 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.1179G>C (p.Arg393Ser) single nucleotide variant Inborn genetic diseases [RCV002724029] Chr20:19685216 [GRCh38]
Chr20:19665860 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.832G>A (p.Gly278Arg) single nucleotide variant Inborn genetic diseases [RCV002722413] Chr20:19681922 [GRCh38]
Chr20:19662566 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.1511C>A (p.Thr504Asn) single nucleotide variant Inborn genetic diseases [RCV003256697] Chr20:19696816 [GRCh38]
Chr20:19677460 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.1315G>A (p.Asp439Asn) single nucleotide variant Inborn genetic diseases [RCV003190217] Chr20:19685352 [GRCh38]
Chr20:19665996 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.817G>A (p.Gly273Arg) single nucleotide variant Inborn genetic diseases [RCV003179489] Chr20:19681907 [GRCh38]
Chr20:19662551 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.1567G>A (p.Val523Met) single nucleotide variant Inborn genetic diseases [RCV003309469] Chr20:19696872 [GRCh38]
Chr20:19677516 [GRCh37]
Chr20:20p11.23		 uncertain significance
GRCh38/hg38 20p13-11.21(chr20:87153-23635465)x3 copy number gain Renal agenesis [RCV003327640] Chr20:87153..23635465 [GRCh38]
Chr20:20p13-11.21		 pathogenic
NM_020689.4(SLC24A3):c.1195C>T (p.Arg399Trp) single nucleotide variant Inborn genetic diseases [RCV003340175] Chr20:19685232 [GRCh38]
Chr20:19665876 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.245G>A (p.Arg82Gln) single nucleotide variant Inborn genetic diseases [RCV003364270] Chr20:19281061 [GRCh38]
Chr20:19261705 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.749T>C (p.Ile250Thr) single nucleotide variant Inborn genetic diseases [RCV003386198] Chr20:19673636 [GRCh38]
Chr20:19654280 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.7C>A (p.Pro3Thr) single nucleotide variant Inborn genetic diseases [RCV003385545] Chr20:19212849 [GRCh38]
Chr20:19193493 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.1129A>G (p.Ile377Val) single nucleotide variant Inborn genetic diseases [RCV003368891] Chr20:19685166 [GRCh38]
Chr20:19665810 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.307G>A (p.Glu103Lys) single nucleotide variant Inborn genetic diseases [RCV003366683] Chr20:19515523 [GRCh38]
Chr20:19496167 [GRCh37]
Chr20:20p11.23		 uncertain significance
NM_020689.4(SLC24A3):c.826G>A (p.Val276Ile) single nucleotide variant not provided [RCV003440355] Chr20:19681916 [GRCh38]
Chr20:19662560 [GRCh37]
Chr20:20p11.23		 uncertain significance
GRCh37/hg19 20p13-11.21(chr20:68351-23860313)x3 copy number gain not provided [RCV003885495] Chr20:68351..23860313 [GRCh37]
Chr20:20p13-11.21		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:726
Count of miRNA genes:496
Interacting mature miRNAs:537
Transcripts:ENST00000328041
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Markers in Region
Z94601  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,396,002 - 19,396,132UniSTSGRCh37
Build 362019,344,002 - 19,344,132RGDNCBI36
Celera2019,470,148 - 19,470,278RGD
Cytogenetic Map20p13UniSTS
HuRef2019,358,487 - 19,358,617UniSTS
Z94352  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,413,068 - 19,413,193UniSTSGRCh37
Build 362019,361,068 - 19,361,193RGDNCBI36
Celera2019,487,204 - 19,487,329RGD
Cytogenetic Map20p13UniSTS
HuRef2019,375,285 - 19,375,410UniSTS
AL031192  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,468,246 - 19,468,396UniSTSGRCh37
Build 362019,416,246 - 19,416,396RGDNCBI36
Celera2019,542,382 - 19,542,532RGD
Cytogenetic Map20p13UniSTS
HuRef2019,430,459 - 19,430,609UniSTS
SHGC-77980  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,663,939 - 19,664,217UniSTSGRCh37
Build 362019,611,939 - 19,612,217RGDNCBI36
Celera2019,738,071 - 19,738,349RGD
Cytogenetic Map20p13UniSTS
HuRef2019,626,527 - 19,626,805UniSTS
SHGC-81264  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,320,080 - 19,320,365UniSTSGRCh37
Build 362019,268,080 - 19,268,365RGDNCBI36
Celera2019,394,223 - 19,394,508RGD
Cytogenetic Map20p13UniSTS
HuRef2019,282,601 - 19,282,886UniSTS
TNG Radiation Hybrid Map2010264.0UniSTS
SHGC-81433  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,559,526 - 19,559,855UniSTSGRCh37
Build 362019,507,526 - 19,507,855RGDNCBI36
Celera2019,633,656 - 19,633,985RGD
Cytogenetic Map20p13UniSTS
HuRef2019,521,767 - 19,522,096UniSTS
TNG Radiation Hybrid Map2010962.0UniSTS
RH118679  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,624,467 - 19,624,761UniSTSGRCh37
Build 362019,572,467 - 19,572,761RGDNCBI36
Celera2019,698,595 - 19,698,889RGD
Cytogenetic Map20p13UniSTS
HuRef2019,586,642 - 19,586,936UniSTS
TNG Radiation Hybrid Map2010908.0UniSTS
RH120551  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,556,220 - 19,556,464UniSTSGRCh37
Build 362019,504,220 - 19,504,464RGDNCBI36
Celera2019,630,350 - 19,630,594RGD
Cytogenetic Map20p13UniSTS
HuRef2019,518,461 - 19,518,705UniSTS
TNG Radiation Hybrid Map2010943.0UniSTS
RH122289  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,485,558 - 19,485,898UniSTSGRCh37
Build 362019,433,558 - 19,433,898RGDNCBI36
Celera2019,559,692 - 19,560,032RGD
Cytogenetic Map20p13UniSTS
HuRef2019,447,790 - 19,448,130UniSTS
TNG Radiation Hybrid Map2011004.0UniSTS
D20S40  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,279,784 - 19,279,956UniSTSGRCh37
Build 362019,227,784 - 19,227,956RGDNCBI36
Celera2019,353,937 - 19,354,115RGD
Cytogenetic Map20p13UniSTS
HuRef2019,242,138 - 19,242,316UniSTS
D20S139  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,646,402 - 19,646,546UniSTSGRCh37
Build 362019,594,402 - 19,594,546RGDNCBI36
Celera2019,720,534 - 19,720,678RGD
Cytogenetic Map20p13UniSTS
HuRef2019,609,174 - 19,609,316UniSTS
SHGC-77737  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,512,072 - 19,512,416UniSTSGRCh37
Build 362019,460,072 - 19,460,416RGDNCBI36
Celera2019,586,205 - 19,586,549RGD
Cytogenetic Map20p13UniSTS
HuRef2019,474,312 - 19,474,656UniSTS
TNG Radiation Hybrid Map2010949.0UniSTS
D20S804  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,556,957 - 19,557,109UniSTSGRCh37
Build 362019,504,957 - 19,505,109RGDNCBI36
Celera2019,631,087 - 19,631,239RGD
Cytogenetic Map20p13UniSTS
HuRef2019,519,198 - 19,519,350UniSTS
G18128  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,267,923 - 19,268,051UniSTSGRCh37
Build 362019,215,923 - 19,216,051RGDNCBI36
Celera2019,342,072 - 19,342,200RGD
Cytogenetic Map20p13UniSTS
HuRef2019,230,271 - 19,230,399UniSTS
Z94382  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,564,530 - 19,564,660UniSTSGRCh37
Build 362019,512,530 - 19,512,660RGDNCBI36
Celera2019,638,660 - 19,638,790RGD
Cytogenetic Map20p13UniSTS
HuRef2019,526,771 - 19,526,901UniSTS
SHGC-102685  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,498,465 - 19,498,737UniSTSGRCh37
Build 362019,446,465 - 19,446,737RGDNCBI36
Celera2019,572,599 - 19,572,871RGD
Cytogenetic Map20p13UniSTS
HuRef2019,460,700 - 19,460,972UniSTS
TNG Radiation Hybrid Map2010984.0UniSTS
Z94579  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,546,714 - 19,546,839UniSTSGRCh37
Build 362019,494,714 - 19,494,839RGDNCBI36
Celera2019,620,845 - 19,620,970RGD
Cytogenetic Map20p13UniSTS
HuRef2019,508,954 - 19,509,079UniSTS
AL031193  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,358,347 - 19,358,490UniSTSGRCh37
Build 362019,306,347 - 19,306,490RGDNCBI36
Celera2019,432,495 - 19,432,638RGD
Cytogenetic Map20p13UniSTS
HuRef2019,320,832 - 19,320,975UniSTS
D20S1040  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,371,567 - 19,371,768UniSTSGRCh37
Build 362019,319,567 - 19,319,768RGDNCBI36
Celera2019,445,714 - 19,445,915RGD
Cytogenetic Map20p13UniSTS
Whitehead-RH Map2095.6UniSTS
WI-11208  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,616,026 - 19,616,200UniSTSGRCh37
Build 362019,564,026 - 19,564,200RGDNCBI36
Celera2019,690,154 - 19,690,328RGD
Cytogenetic Map20p13UniSTS
HuRef2019,578,200 - 19,578,374UniSTS
Whitehead-RH Map2087.1UniSTS
AL031209  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,353,995 - 19,354,116UniSTSGRCh37
Build 362019,301,995 - 19,302,116RGDNCBI36
Celera2019,428,143 - 19,428,264RGD
Cytogenetic Map20p13UniSTS
HuRef2019,316,480 - 19,316,601UniSTS
A008U36  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,702,056 - 19,702,190UniSTSGRCh37
Build 362019,650,056 - 19,650,190RGDNCBI36
Celera2019,776,151 - 19,776,285RGD
Cytogenetic Map20p13UniSTS
HuRef2019,664,751 - 19,664,885UniSTS
GeneMap99-GB4 RH Map20105.9UniSTS
NCBI RH Map20161.8UniSTS
Z94614  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,253,158 - 19,253,254UniSTSGRCh37
Build 362019,201,158 - 19,201,254RGDNCBI36
Celera2019,327,305 - 19,327,401RGD
Cytogenetic Map20p11.23UniSTS
Cytogenetic Map20p13UniSTS
HuRef2019,215,583 - 19,215,679UniSTS
SHGC-32038  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,703,394 - 19,703,519UniSTSGRCh37
Build 362019,651,394 - 19,651,519RGDNCBI36
Celera2019,777,489 - 19,777,614RGD
Cytogenetic Map20p13UniSTS
HuRef2019,666,089 - 19,666,214UniSTS
GeneMap99-GB4 RH Map20106.42UniSTS
GeneMap99-GB4 RH Map20105.19UniSTS
Whitehead-RH Map2097.4UniSTS
GeneMap99-G3 RH Map201041.0UniSTS
Z94345  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,644,304 - 19,644,453UniSTSGRCh37
Build 362019,592,304 - 19,592,453RGDNCBI36
Celera2019,718,436 - 19,718,585RGD
Cytogenetic Map20p13UniSTS
HuRef2019,607,076 - 19,607,225UniSTS
Z94526  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372019,488,663 - 19,488,805UniSTSGRCh37
Build 362019,436,663 - 19,436,805RGDNCBI36
Celera2019,562,797 - 19,562,939RGD
Cytogenetic Map20p13UniSTS
HuRef2019,450,895 - 19,451,037UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 1037 1311 161 59 88 9 2299 894 1640 43 778 517 51 735 1598 1
Low 1301 1200 1304 322 1108 211 1978 1025 2030 284 601 952 117 1 469 1189 3 1
Below cutoff 36 472 220 211 373 213 33 264 19 59 29 65 3 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000328041   ⟹   ENSP00000333519
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2019,212,642 - 19,722,926 (+)Ensembl
RefSeq Acc Id: ENST00000613834   ⟹   ENSP00000482967
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2019,212,843 - 19,722,899 (+)Ensembl
RefSeq Acc Id: NM_020689   ⟹   NP_065740
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382019,212,642 - 19,722,926 (+)NCBI
GRCh372019,193,290 - 19,703,541 (+)RGD
Build 362019,141,290 - 19,651,541 (+)NCBI Archive
Celera2019,267,475 - 19,777,636 (+)RGD
HuRef2019,155,790 - 19,666,236 (+)RGD
CHM1_12019,262,244 - 19,704,077 (+)NCBI
T2T-CHM13v2.02019,264,159 - 19,774,968 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_065740 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAG12988 (Get FASTA)   NCBI Sequence Viewer  
  EAX10219 (Get FASTA)   NCBI Sequence Viewer  
  EAX10220 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000333519
  ENSP00000333519.5
GenBank Protein Q9HC58 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_065740   ⟸   NM_020689
- Peptide Label: precursor
- UniProtKB: Q9BQY3 (UniProtKB/Swiss-Prot),   Q9BQL7 (UniProtKB/Swiss-Prot),   Q9BQJ9 (UniProtKB/Swiss-Prot),   B1AKV7 (UniProtKB/Swiss-Prot),   Q9H519 (UniProtKB/Swiss-Prot),   Q9HC58 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000482967   ⟸   ENST00000613834
RefSeq Acc Id: ENSP00000333519   ⟸   ENST00000328041

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9HC58-F1-model_v2 AlphaFold Q9HC58 1-644 view protein structure

Promoters
RGD ID:6799065
Promoter ID:HG_KWN:38757
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:NB4
Transcripts:OTTHUMT00000078207
Position:
Human AssemblyChrPosition (strand)Source
Build 362019,141,076 - 19,141,576 (+)MPROMDB
RGD ID:13206483
Promoter ID:EPDNEW_H26822
Type:initiation region
Name:SLC24A3_1
Description:solute carrier family 24 member 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H26821  EPDNEW_H26823  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382019,212,515 - 19,212,575EPDNEW
RGD ID:13206485
Promoter ID:EPDNEW_H26823
Type:initiation region
Name:SLC24A3_2
Description:solute carrier family 24 member 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H26821  EPDNEW_H26822  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382019,212,737 - 19,212,797EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:10977 AgrOrtholog
COSMIC SLC24A3 COSMIC
Ensembl Genes ENSG00000185052 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000328041 ENTREZGENE
  ENST00000328041.11 UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.1420.30 UniProtKB/Swiss-Prot
GTEx ENSG00000185052 GTEx
HGNC ID HGNC:10977 ENTREZGENE
Human Proteome Map SLC24A3 Human Proteome Map
InterPro K/Na/Ca-exchanger UniProtKB/Swiss-Prot
  NaCa_Exmemb UniProtKB/Swiss-Prot
  NCX_ion-bd_dom_sf UniProtKB/Swiss-Prot
KEGG Report hsa:57419 UniProtKB/Swiss-Prot
NCBI Gene 57419 ENTREZGENE
OMIM 609839 OMIM
PANTHER PTHR10846 UniProtKB/Swiss-Prot
  SODIUM/POTASSIUM/CALCIUM EXCHANGER 3 UniProtKB/Swiss-Prot
Pfam Na_Ca_ex UniProtKB/Swiss-Prot
PharmGKB PA35853 PharmGKB
UniProt B1AKV7 ENTREZGENE
  NCKX3_HUMAN UniProtKB/Swiss-Prot
  Q9BQJ9 ENTREZGENE
  Q9BQL7 ENTREZGENE
  Q9BQY3 ENTREZGENE
  Q9H519 ENTREZGENE
  Q9HC58 ENTREZGENE
UniProt Secondary B1AKV7 UniProtKB/Swiss-Prot
  Q9BQJ9 UniProtKB/Swiss-Prot
  Q9BQL7 UniProtKB/Swiss-Prot
  Q9BQY3 UniProtKB/Swiss-Prot
  Q9H519 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-23 SLC24A3  solute carrier family 24 member 3    solute carrier family 24 (sodium/potassium/calcium exchanger), member 3  Symbol and/or name change 5135510 APPROVED
2011-09-01 SLC24A3  solute carrier family 24 (sodium/potassium/calcium exchanger), member 3  SLC24A3  solute carrier family 24 (sodium/potassium/calcium exchanger), member 3  Symbol and/or name change 5135510 APPROVED