Human Gene NHERF1 (ENST00000262613.10_4) from GENCODE V47lift37
  Description: SLC9A3 regulator 1 (from RefSeq NM_004252.5)
Gencode Transcript: ENST00000262613.10_4
Gencode Gene: ENSG00000109062.12_13
Transcript (Including UTRs)
   Position: hg19 chr17:72,744,767-72,765,492 Size: 20,726 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr17:72,744,986-72,764,795 Size: 19,810 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:72,744,767-72,765,492)mRNA (may differ from genome)Protein (358 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
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OMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NHRF1_HUMAN
DESCRIPTION: RecName: Full=Na(+)/H(+) exchange regulatory cofactor NHE-RF1; Short=NHERF-1; AltName: Full=Ezrin-radixin-moesin-binding phosphoprotein 50; Short=EBP50; AltName: Full=Regulatory cofactor of Na(+)/H(+) exchanger; AltName: Full=Sodium-hydrogen exchanger regulatory factor 1; AltName: Full=Solute carrier family 9 isoform A3 regulatory factor 1;
FUNCTION: Scaffold protein that connects plasma membrane proteins with members of the ezrin/moesin/radixin family and thereby helps to link them to the actin cytoskeleton and to regulate their surface expression. Necessary for recycling of internalized ADRB2. Was first known to play a role in the regulation of the activity and subcellular location of SLC9A3. Necessary for cAMP-mediated phosphorylation and inhibition of SLC9A3. May enhance Wnt signaling. May participate in HTR4 targeting to microvilli (By similarity). Involved in the regulation of phosphate reabsorption in the renal proximal tubules.
SUBUNIT: Homodimer, and heterodimer with SLC9A3R2. Binds the N- termini of EZR, RDX and MSN. Binds the C-termini of PDGFRA, PDGFRB, ADRB2, NOS2 and CFTR. Binds ARHGAP17, EPI64, GNB2L1, OPRK1, GNAQ, CTNNB1 and PLCB3. Binds PDZK1 (By similarity). Interacts with CLCN3. Binds the C-terminus of PAG1. In resting T- cells, part of a PAG1-SLC9A3R1-MSN complex which is disrupted upon TCR activation. Forms a complex with CFTR and SLC4A7. Forms a complex with SLC4A7 and ATP6V1B1. Interacts with TRPC4 (via the PDZ-binding domain). Directly interacts with HTR4 (By similarity). Interacts (via the PDZ 1 domain) with PODXL (via the C-terminal PDZ-binding motif DTHL); interaction is not detected in glomerular epithelium cells. Interacts (via the PDZ 1 domain) with PODXL (via the C-terminal PDZ-binding motif DTHL); the interaction take place early in the secretory pathway and is necessary for its apical membrane sorting (By similarity). Interacts with MCC. Interacts with SLC34A1.
INTERACTION: P13569:CFTR; NbExp=2; IntAct=EBI-349787, EBI-349854; P26038:MSN; NbExp=5; IntAct=EBI-349787, EBI-528768; P35240-1:NF2; NbExp=4; IntAct=EBI-349787, EBI-1014500;
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Apical cell membrane (By similarity). Endomembrane system; Peripheral membrane protein. Cell projection, filopodium. Cell projection, ruffle. Cell projection, microvillus. Note=Translocates from the cytoplasm to the apical cell membrane in a PODXL-dependent manner (By similarity). Colocalizes with actin in microvilli-rich apical regions of the syncytiotrophoblast. Found in microvilli, ruffling membrane and filopodia of HeLa cells. Present in lipid rafts of T- cells.
TISSUE SPECIFICITY: Detected in liver, kidney, pancreas, prostate, spleen, small intestine and placenta, in particular in the syncytiotrophoblast.
INDUCTION: By estrogen.
PTM: Phosphorylated on serine residues.
DISEASE: Defects in SLC9A3R1 are the cause of hypophosphatemic nephrolithiasis/osteoporosis type 2 (NPHLOP2) [MIM:612287]. Hypophosphatemia results from idiopathic renal phosphate loss. It contributes to the pathogenesis of hypophosphatemic urolithiasis (formation of urinary calculi) as well to that of hypophosphatemic osteoporosis (bone demineralization).
SIMILARITY: Contains 2 PDZ (DHR) domains.
SEQUENCE CAUTION: Sequence=AAH49220.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

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+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 191.30 RPKM in Esophagus - Mucosa
Total median expression: 1854.38 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -112.90219-0.516 Picture PostScript Text
3' UTR -223.00697-0.320 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR015098 - EBP50_C-term
IPR017300 - NaH_exchngr_reg_CF_NHE-RF
IPR001478 - PDZ

Pfam Domains:
PF00595 - PDZ domain
PF09007 - EBP50, C-terminal
PF17820 - PDZ domain

SCOP Domains:
50156 - PDZ domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1G9O - X-ray MuPIT 1GQ4 - X-ray MuPIT 1GQ5 - X-ray MuPIT 1I92 - X-ray MuPIT 1SGH - X-ray MuPIT 2D10 - X-ray 2JXO - NMR MuPIT 2KJD - NMR MuPIT 2KRG - NMR MuPIT 2OZF - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O14745
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005515 protein binding
GO:0008013 beta-catenin binding
GO:0017081 chloride channel regulator activity
GO:0019902 phosphatase binding
GO:0019904 protein domain specific binding
GO:0030165 PDZ domain binding
GO:0031698 beta-2 adrenergic receptor binding
GO:0032947 protein complex scaffold
GO:0043621 protein self-association
GO:0044877 macromolecular complex binding
GO:0045159 myosin II binding
GO:0050780 dopamine receptor binding
GO:0070851 growth factor receptor binding

Biological Process:
GO:0003096 renal sodium ion transport
GO:0007097 nuclear migration
GO:0007191 adenylate cyclase-activating dopamine receptor signaling pathway
GO:0007605 sensory perception of sound
GO:0008285 negative regulation of cell proliferation
GO:0008360 regulation of cell shape
GO:0008361 regulation of cell size
GO:0010642 negative regulation of platelet-derived growth factor receptor signaling pathway
GO:0010766 negative regulation of sodium ion transport
GO:0014067 negative regulation of phosphatidylinositol 3-kinase signaling
GO:0016055 Wnt signaling pathway
GO:0019933 cAMP-mediated signaling
GO:0022612 gland morphogenesis
GO:0030033 microvillus assembly
GO:0030036 actin cytoskeleton organization
GO:0030336 negative regulation of cell migration
GO:0030643 cellular phosphate ion homeostasis
GO:0032415 regulation of sodium:proton antiporter activity
GO:0032416 negative regulation of sodium:proton antiporter activity
GO:0032782 bile acid secretion
GO:0034613 cellular protein localization
GO:0034635 glutathione transport
GO:0044062 regulation of excretion
GO:0045198 establishment of epithelial cell apical/basal polarity
GO:0045859 regulation of protein kinase activity
GO:0045930 negative regulation of mitotic cell cycle
GO:0051683 establishment of Golgi localization
GO:0051898 negative regulation of protein kinase B signaling
GO:0060088 auditory receptor cell stereocilium organization
GO:0060158 phospholipase C-activating dopamine receptor signaling pathway
GO:0065003 macromolecular complex assembly
GO:0070293 renal absorption
GO:0070373 negative regulation of ERK1 and ERK2 cascade
GO:0072659 protein localization to plasma membrane
GO:0090090 negative regulation of canonical Wnt signaling pathway
GO:0097291 renal phosphate ion absorption
GO:2000146 negative regulation of cell motility
GO:2001244 positive regulation of intrinsic apoptotic signaling pathway

Cellular Component:
GO:0001726 ruffle
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0005902 microvillus
GO:0012505 endomembrane system
GO:0015629 actin cytoskeleton
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0030175 filopodium
GO:0031526 brush border membrane
GO:0031528 microvillus membrane
GO:0031982 vesicle
GO:0032420 stereocilium
GO:0032426 stereocilium tip
GO:0042995 cell projection
GO:0045121 membrane raft
GO:0045177 apical part of cell
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome
GO:0071944 cell periphery
GO:0097225 sperm midpiece
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK312498 - Homo sapiens cDNA, FLJ92860, highly similar to Homo sapiens solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1 (SLC9A3R1), mRNA.
AK094467 - Homo sapiens cDNA FLJ37148 fis, clone BRACE2025333, highly similar to Homo sapiens Na+/H+ exchange regulatory co-factor (NHERF) mRNA.
AK128474 - Homo sapiens cDNA FLJ46618 fis, clone TLIVE2007736, highly similar to Ezrin-radixin-moesin-binding phosphoprotein 50.
AK026581 - Homo sapiens cDNA: FLJ22928 fis, clone KAT07089, highly similar to AF015926 Homo sapiens ezrin-radixin-moesin binding phosphoprotein-50 mRNA.
BC049220 - Homo sapiens solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1, mRNA (cDNA clone IMAGE:5496466), partial cds.
BC003361 - Homo sapiens solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1, mRNA (cDNA clone MGC:5270 IMAGE:2900516), complete cds.
AF015926 - Homo sapiens ezrin-radixin-moesin binding phosphoprotein-50 mRNA, complete cds.
BC011777 - Homo sapiens solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1, mRNA (cDNA clone MGC:19770 IMAGE:3640162), complete cds.
BC053350 - Homo sapiens solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1, mRNA (cDNA clone MGC:61480 IMAGE:5218414), complete cds.
BC001443 - Homo sapiens solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1, mRNA (cDNA clone MGC:1482 IMAGE:3138881), complete cds.
AF036241 - Homo sapiens Na+/H+ exchange regulatory co-factor (NHERF) mRNA, complete cds.
HZ409100 - JP 2015528002-A/1697: CHIRAL CONTROL.
LG052434 - KR 1020150036642-A/1700: CHIRAL CONTROL.
DL491243 - Novel nucleic acids.
HZ082966 - JP 2015513906-A/323: Stem Cell Microparticles.
HZ436747 - JP 2015529450-A/323: Stem Cell Microparticles.
HZ480259 - JP 2015535430-A/765: TERMINALLY MODIFIED RNA.
HZ790190 - JP 2016504050-A/1935: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
JC171951 - Sequence 323 from Patent WO2013150303.
JC512922 - Sequence 3175 from Patent WO2014113089.
JC572762 - Sequence 323 from Patent WO2014125276.
JC582450 - Sequence 323 from Patent WO2014125277.
JE954146 - Sequence 323 from Patent WO2015052526.
JE955899 - Sequence 323 from Patent WO2015052527.
LF137651 - JP 2016507550-A/323: Method of Producing Microparticles.
LF160480 - JP 2016513950-A/546: Oligomers with improved off-target profile.
LF162616 - JP 2016513095-A/323: Stem Cell Microparticles and miRNA.
LF953368 - JP 2016534103-A/323: Stem Cell Microparticles and miRNA.
LG005713 - KR 1020150004822-A/323: STEM CELL MICROPARTICLES.
LG053409 - KR 1020150059168-A/323: STEM CELL MICROPARTICLES.
LG240648 - KR 1020160035087-A/323: STEM CELL MICROPARTICLES AND MIRNA.
LP835283 - Sequence 81 from Patent WO2017108535.
LP939590 - Sequence 81 from Patent EP3184646.
LQ070510 - Sequence 834 from Patent EP2964234.
LV470733 - JP 2016534036-A/323: Stem Cell Microparticles and miRNA.
LY267871 - KR 1020160137115-A/1: Use of Micro RNAs of miR-3615, miR-5701, miR-5581-3p, miR-4792 and miR-2467-5p for Diagnosis of Chronic Obstructive Pulmonary Disease.
DL489889 - Novel nucleic acids.
JD289215 - Sequence 270239 from Patent EP1572962.
JD396516 - Sequence 377540 from Patent EP1572962.
MA644011 - JP 2017113010-A/1935: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA731895 - JP 2017140048-A/765: TERMINALLY MODIFIED RNA.
MP015325 - Sequence 528 from Patent WO2019016252.
MA801064 - JP 2018183181-A/1935: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MP129423 - Sequence 323 from Patent EP3470073.
MP162346 - Sequence 323 from Patent WO2019069093.
MP168057 - Sequence 64 from Patent EP3469101.
MB120026 - WO 2019117306-A/48: Method of aiding detection of Alzheimer's disease.
MB481484 - JP 2019528758-A/64: Methods And Compositions For Prostate Cancer Diagnosis And Treatment.
MP395089 - Sequence 187 from Patent EP3565903.
AB528945 - Synthetic construct DNA, clone: pF1KE0795, Homo sapiens SLC9A3R1 gene for solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1, without stop codon, in Flexi system.
KJ892757 - Synthetic construct Homo sapiens clone ccsbBroadEn_02151 SLC9A3R1 gene, encodes complete protein.
KR709325 - Synthetic construct Homo sapiens clone CCSBHm_00000252 SLC9A3R1 (SLC9A3R1) mRNA, encodes complete protein.
KR709326 - Synthetic construct Homo sapiens clone CCSBHm_00000253 SLC9A3R1 (SLC9A3R1) mRNA, encodes complete protein.
BX648303 - Homo sapiens mRNA; cDNA DKFZp686A10131 (from clone DKFZp686A10131).
JD162900 - Sequence 143924 from Patent EP1572962.
JD115753 - Sequence 96777 from Patent EP1572962.
JD453318 - Sequence 434342 from Patent EP1572962.
JD404255 - Sequence 385279 from Patent EP1572962.
JD300131 - Sequence 281155 from Patent EP1572962.
JD124649 - Sequence 105673 from Patent EP1572962.
JD398462 - Sequence 379486 from Patent EP1572962.
JD119000 - Sequence 100024 from Patent EP1572962.
JD082462 - Sequence 63486 from Patent EP1572962.
JD479555 - Sequence 460579 from Patent EP1572962.
JD062005 - Sequence 43029 from Patent EP1572962.
JD420634 - Sequence 401658 from Patent EP1572962.
JD288694 - Sequence 269718 from Patent EP1572962.
JD186482 - Sequence 167506 from Patent EP1572962.
JD066489 - Sequence 47513 from Patent EP1572962.
JD475761 - Sequence 456785 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_cftrPathway - Cystic fibrosis transmembrane conductance regulator (CFTR) and beta 2 adrenergic receptor (b2AR) pathway

-  Other Names for This Gene
  Alternate Gene Symbols: B3KY21, ENST00000262613.1, ENST00000262613.2, ENST00000262613.3, ENST00000262613.4, ENST00000262613.5, ENST00000262613.6, ENST00000262613.7, ENST00000262613.8, ENST00000262613.9, NHERF, NHERF1 , NHRF1_HUMAN, NM_004252, O14745, O43552, Q86WQ5, SLC9A3R1, uc317hby.1, uc317hby.2
UCSC ID: ENST00000262613.10_4
RefSeq Accession: NM_004252.5
Protein: O14745 (aka NHRF1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.