NHERF4

gene
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Also known as FLJ22756IKEPPNaPi-Cap2

Summary

NHERF4 (NHERF family PDZ scaffold protein 4, HGNC:19891) is a protein-coding gene on chromosome 11q23.3, encoding Na(+)/H(+) exchange regulatory cofactor NHE-RF4 (Q86UT5). Acts as a regulatory protein that associates with GUCY2C and negatively modulates its heat-stable enterotoxin-mediated activation.

Guanylyl cyclase C (GCC, or GUCY2C; MIM 601330) produces cGMP following the binding of either endogenous ligands or heat-stable enterotoxins secreted by E. coli and other enteric bacteria. Activation of GCC initiates a signaling cascade that leads to phosphorylation of the cystic fibrosis transmembrane conductance regulator (CFTR; MIM 602421), followed by a net efflux of ions and water into the intestinal lumen. IKEPP is a regulatory protein that associates with GCC and regulates the amount of cGMP produced following receptor stimulation (Scott et al., 2002 [PubMed 11950846]).

Source: NCBI Gene 79849 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 103 total
  • MANE Select transcript: NM_001168468

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19891
Approved symbolNHERF4
NameNHERF family PDZ scaffold protein 4
Location11q23.3
Locus typegene with protein product
StatusApproved
AliasesFLJ22756, IKEPP, NaPi-Cap2
Ensembl geneENSG00000172367
Ensembl biotypeprotein_coding
OMIM607146
Entrez79849

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 retained_intron, 4 protein_coding, 1 nonsense_mediated_decay

ENST00000322712, ENST00000355547, ENST00000525131, ENST00000526279, ENST00000526836, ENST00000527028, ENST00000527308, ENST00000527951, ENST00000528730, ENST00000529098, ENST00000529573, ENST00000531114, ENST00000533688, ENST00000534790

RefSeq mRNA: 2 — MANE Select: NM_001168468 NM_001168468, NM_024791

CCDS: CCDS53719, CCDS8417

Canonical transcript exons

ENST00000355547 — 11 exons

ExonStartEnd
ENSE00001243980119188355119188551
ENSE00001243987119187940119188144
ENSE00003509001119187564119187700
ENSE00003519123119187270119187459
ENSE00003535270119188640119188867
ENSE00003609116119186092119186165
ENSE00003617440119189005119189205
ENSE00003622123119185925119185952
ENSE00003656219119186479119186690
ENSE00003847504119185475119185510
ENSE00003848671119189463119190213

Expression profiles

Bgee: expression breadth ubiquitous, 129 present calls, max score 95.92.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2308 / max 69.0380, expressed in 35 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1171040.183231
1171030.041119
1171020.00644

Top tissues by expression

256 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
mucosa of transverse colonUBERON:000499195.92gold quality
duodenumUBERON:000211491.43gold quality
rectumUBERON:000105291.35gold quality
ileal mucosaUBERON:000033190.70gold quality
right uterine tubeUBERON:000130288.46gold quality
jejunal mucosaUBERON:000039987.44gold quality
small intestine Peyer’s patchUBERON:000345487.31gold quality
small intestineUBERON:000210886.50gold quality
transverse colonUBERON:000115786.02gold quality
adult mammalian kidneyUBERON:000008284.19gold quality
gall bladderUBERON:000211083.51gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047379.71gold quality
buccal mucosa cellCL:000233678.72gold quality
colonic mucosaUBERON:000031778.59gold quality
jejunumUBERON:000211578.50gold quality
triceps brachiiUBERON:000150978.22gold quality
kidneyUBERON:000211378.22gold quality
gluteal muscleUBERON:000200077.83gold quality
cervix squamous epitheliumUBERON:000692277.71gold quality
pancreatic ductal cellCL:000207977.60silver quality
mucosa of sigmoid colonUBERON:000499377.05gold quality
intestineUBERON:000016075.82gold quality
kidney epitheliumUBERON:000481973.72silver quality
nephron tubuleUBERON:000123173.66silver quality
cortex of kidneyUBERON:000122573.58gold quality
cerebellar vermisUBERON:000472073.46gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450273.25gold quality
large intestineUBERON:000005972.39gold quality
endothelial cellCL:000011572.31gold quality
metanephros cortexUBERON:001053372.21gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting NHERF4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-4659A-3P99.8072.624248
HSA-MIR-4659B-3P99.8072.624248
HSA-MIR-431999.7669.832586
HSA-MIR-1212499.6869.172700
HSA-MIR-427699.5667.662514
HSA-MIR-519D-5P99.4169.302057
HSA-MIR-125A-5P99.3670.591640
HSA-MIR-125B-5P99.3670.361662
HSA-MIR-6811-3P98.6266.54944
HSA-MIR-3135B98.6165.331470
HSA-MIR-210-5P98.5764.37832
HSA-MIR-5008-5P98.4265.871019
HSA-MIR-654-3P98.3867.61905
HSA-MIR-286195.2465.471056
HSA-MIR-6769A-3P94.9161.36412
HSA-MIR-807490.6165.46165

Literature-anchored findings (GeneRIF, showing 4)

  • A novel PDZ protein regulates the activity of guanylyl cyclase C, the heat-stable enterotoxin receptor. (PMID:11950846)
  • Regulation of NHE3 depends on the nature of the NHERF family member associating with NHE3 and the accompanying NHE3 complexes. (PMID:19088451)
  • The NHERF4 is a novel modulator of luminal fluidity in the intestine by adjusting SLC26A3 expression and activity through a phosphorylation-dependent mechanism. (PMID:22627094)
  • IKEPP was also found to be expressed in vascular endothelial cells where it co-localizes and complexes with the hIP (PMID:22884631)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerionherf4aENSDARG00000040568
danio_rerionherf4bENSDARG00000055656
mus_musculusNherf4ENSMUSG00000032105
rattus_norvegicusNherf4ENSRNOG00000008526
caenorhabditis_elegansWBGENE00006438

Paralogs (3): NHERF2 (ENSG00000065054), NHERF1 (ENSG00000109062), PDZK1 (ENSG00000174827)

Protein

Protein identifiers

Na(+)/H(+) exchange regulatory cofactor NHE-RF4Q86UT5 (reviewed: Q86UT5)

Alternative names: Intestinal and kidney-enriched PDZ protein, Natrium-phosphate cotransporter IIa C-terminal-associated protein 2, PDZ domain-containing protein 2, PDZ domain-containing protein 3, Sodium-hydrogen exchanger regulatory factor 4

All UniProt accessions (4): B0YJ61, E9PPZ1, E9PRB0, Q86UT5

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a regulatory protein that associates with GUCY2C and negatively modulates its heat-stable enterotoxin-mediated activation. Stimulates SLC9A3 activity in the presence of elevated calcium ions.

Subunit / interactions. Interacts with the C-terminal region of GUCY2C. Interacts with the C-terminal region SLC9A3 and the interactions decrease in response to elevated calcium ion levels. Interacts with the C-terminal region of SLC34A1. Interacts with USP2 isoform 4. Interacts (via the third PDZ domain) with SLC26A3 (via PDZ-binding motif); interaction leads to decreased expression of SLC26A3 on the cell membrane resulting in its reduced exchanger activity.

Subcellular location. Cell membrane. Cytoplasm.

Tissue specificity. Expressed in kidney and the gastrointestinal tract. Not detected in brain, heart, skeletal muscle or cells of hematopoietic origin.

Post-translational modifications. Phosphorylation at Ser-395 negatively regulates its interaction with SLC26A3.

Isoforms (5)

UniProt IDNamesCanonical?
Q86UT5-11yes
Q86UT5-22
Q86UT5-33
Q86UT5-44
Q86UT5-55

RefSeq proteins (2): NP_001161940, NP_079067 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001478PDZDomain
IPR036034PDZ_sfHomologous_superfamily
IPR051067NHERFamily

Pfam: PF00595

UniProt features (27 total): splice variant 6, strand 5, domain 4, sequence conflict 4, helix 2, region of interest 2, chain 1, turn 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2V90X-RAY DIFFRACTION2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86UT5-F169.720.27

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 395

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-8942233Intestinal infectious diseases

MSigDB gene sets: 105 (showing top): GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, COUP_01, GOBP_WATER_TRANSPORT, HNF4_DR1_Q3, HNF4_01, PPAR_DR1_Q2, GOCC_APICAL_PLASMA_MEMBRANE, SABATES_COLORECTAL_ADENOMA_DN, GOBP_RESPONSE_TO_TOXIC_SUBSTANCE, GOMF_SIGNALING_RECEPTOR_BINDING, GOCC_CELL_CELL_JUNCTION, GOBP_LOCALIZATION_WITHIN_MEMBRANE, GOBP_FLUID_TRANSPORT, GOCC_APICAL_PART_OF_CELL, GOCC_CLUSTER_OF_ACTIN_BASED_CELL_PROJECTIONS

GO Biological Process (6): monoatomic ion transport (GO:0006811), water transport (GO:0006833), receptor guanylyl cyclase signaling pathway (GO:0007168), response to toxic substance (GO:0009636), negative regulation of receptor guanylyl cyclase signaling pathway (GO:0010754), protein localization to plasma membrane (GO:0072659)

GO Molecular Function (6): signaling receptor binding (GO:0005102), ion channel inhibitor activity (GO:0008200), guanylate cyclase inhibitor activity (GO:0030251), protein-membrane adaptor activity (GO:0043495), ubiquitin-specific protease binding (GO:1990381), protein binding (GO:0005515)

GO Cellular Component (8): cytosol (GO:0005829), plasma membrane (GO:0005886), brush border (GO:0005903), apical plasma membrane (GO:0016324), apical junction complex (GO:0043296), apical part of cell (GO:0045177), cytoplasm (GO:0005737), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Uptake and actions of bacterial toxins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
apical part of cell2
transport1
fluid transport1
enzyme-linked receptor protein signaling pathway1
response to chemical1
receptor guanylyl cyclase signaling pathway1
negative regulation of signal transduction1
protein localization to membrane1
protein localization to cell periphery1
protein binding1
monoatomic ion channel activity1
channel inhibitor activity1
transmembrane transporter binding1
ion channel regulator activity1
guanylate cyclase activity1
cyclase inhibitor activity1
guanylate cyclase regulator activity1
protein-macromolecule adaptor activity1
protease binding1
binding1
cytoplasm1
membrane1
cell periphery1
microvillus1
cluster of actin-based cell projections1
plasma membrane region1
cell-cell junction1
intracellular anatomical structure1

Protein interactions and networks

STRING

822 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NHERF4GUCY2CP25092914
NHERF4CFTRP13569832
NHERF4SLC34A1Q06495737
NHERF4NPR3P17342730
NHERF4SLC22A5O76082640
NHERF4SLC26A3P40879631
NHERF4SLC22A4Q9H015601
NHERF4SHANK2Q9UPX8594
NHERF4GUCA2BQ16661568
NHERF4GOPCQ9HD26568
NHERF4SPRYD7Q5W111565
NHERF4SLC9A3P48764507
NHERF4NHERF1O14745477
NHERF4PDZK1Q5T2W1460
NHERF4GUCA2AQ02747459

IntAct

837 interactions, top by confidence:

ABTypeScore
PRKAG2PRKAB2psi-mi:“MI:0914”(association)0.730
CACNA1SNHERF4psi-mi:“MI:0915”(physical association)0.560
NHERF4SPRYD7psi-mi:“MI:0915”(physical association)0.560
ASAP3NHERF4psi-mi:“MI:0915”(physical association)0.560
NHERF4SLC41A3psi-mi:“MI:0915”(physical association)0.560
NHERF4CACNA1Spsi-mi:“MI:0915”(physical association)0.560
SPRYD7NHERF4psi-mi:“MI:0915”(physical association)0.560
NHERF4ASAP3psi-mi:“MI:0915”(physical association)0.560
SLC41A3NHERF4psi-mi:“MI:0915”(physical association)0.560
E6NHERF4psi-mi:“MI:0915”(physical association)0.540
E6NHERF4psi-mi:“MI:0407”(direct interaction)0.540
PTTG2NHERF4psi-mi:“MI:0407”(direct interaction)0.440
WHRNNHERF4psi-mi:“MI:0407”(direct interaction)0.440
GARIN6NHERF4psi-mi:“MI:0407”(direct interaction)0.440
CIB2NHERF4psi-mi:“MI:0407”(direct interaction)0.440
SLCO1C1NHERF4psi-mi:“MI:0407”(direct interaction)0.440
KCNV1NHERF4psi-mi:“MI:0407”(direct interaction)0.440
SLC15A5NHERF4psi-mi:“MI:0407”(direct interaction)0.440
PRKNNHERF4psi-mi:“MI:0407”(direct interaction)0.440
NHERF4ORF putative E6psi-mi:“MI:0407”(direct interaction)0.440
ABCC4NHERF4psi-mi:“MI:0407”(direct interaction)0.440
GJC1NHERF4psi-mi:“MI:0407”(direct interaction)0.440
DOCK4NHERF4psi-mi:“MI:0407”(direct interaction)0.440
WWTR1NHERF4psi-mi:“MI:0407”(direct interaction)0.440
YAP1NHERF4psi-mi:“MI:0407”(direct interaction)0.440
ASIC3NHERF4psi-mi:“MI:0407”(direct interaction)0.440

BioGRID (17): PDZD3 (Two-hybrid), PDZD3 (Two-hybrid), PDZD3 (Two-hybrid), PDZD3 (Two-hybrid), PDZD3 (Reconstituted Complex), PDZD3 (Reconstituted Complex), PDZD3 (Two-hybrid), PDZD3 (Two-hybrid), PDZD3 (Two-hybrid), PDZD3 (Reconstituted Complex), GUCY2C (Reconstituted Complex), PDZD3 (Affinity Capture-Western), PDZD3 (Protein-peptide), PDZD3 (Affinity Capture-MS), PDZD3 (Two-hybrid)

ESM2 similar proteins: A3R064, A7E3N7, D3ZBP4, E9Q6X9, F1MH07, G3V8H4, O70248, O88888, O95382, O96018, P97465, Q0VBL6, Q13470, Q3KR16, Q3MIN7, Q3UYI5, Q3V3V9, Q4QQV2, Q58EX7, Q5EA84, Q5VV41, Q6F5E8, Q6P5Z2, Q6PGG2, Q80XL1, Q86UT5, Q8BWA8, Q8CJ00, Q8IW93, Q8K031, Q8K045, Q8R5F8, Q8TDZ2, Q8TE67, Q8VDP3, Q924T7, Q92502, Q92918, Q969H4, Q99704

Diamond homologs: A0A140LI67, A0A8P0N4K0, A4D2P6, A5PKA5, A8MUH7, B7WN72, D3YZU1, G5ECY0, O08774, O14745, O14910, O14924, O15085, O88951, O88952, P31016, P70175, P70441, P78352, Q0P5F3, Q12923, Q13425, Q14160, Q15599, Q15700, Q28619, Q28C55, Q2KIB6, Q32LM6, Q3SZK8, Q3T0X8, Q3UHD6, Q4ACU6, Q4H4B6, Q4KL35, Q4R6G4, Q52KW0, Q5F425, Q5F488, Q5PYH5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 118 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
TCF dependent signaling in response to WNT68.6×9e-03
Neuronal System94.9×9e-03

GO biological processes:

GO termPartnersFoldFDR
bicellular tight junction assembly515.2×6e-03
positive regulation of osteoblast differentiation510.3×9e-03
negative regulation of canonical Wnt signaling pathway77.6×6e-03
chemical synaptic transmission96.4×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

103 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance94
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1972 predictions. Top by Δscore:

VariantEffectΔscore
11:119187697:G:GTdonor_gain1.0000
11:119187698:A:Tdonor_gain1.0000
11:119188143:TGG:Tdonor_loss1.0000
11:119188144:GGT:Gdonor_loss1.0000
11:119188145:GT:Gdonor_loss1.0000
11:119188146:T:Adonor_loss1.0000
11:119187427:A:Gdonor_gain0.9900
11:119187434:T:TAdonor_gain0.9900
11:119187435:G:GAdonor_gain0.9900
11:119187559:TCTA:Tacceptor_loss0.9900
11:119187560:CTA:Cacceptor_loss0.9900
11:119187561:TA:Tacceptor_loss0.9900
11:119187562:A:AGacceptor_gain0.9900
11:119187563:G:GGacceptor_gain0.9900
11:119187696:GGAAG:Gdonor_gain0.9900
11:119187697:GAAGG:Gdonor_loss0.9900
11:119187698:AAGG:Adonor_loss0.9900
11:119187699:AGGTG:Adonor_loss0.9900
11:119187700:GGTG:Gdonor_loss0.9900
11:119187937:CAGCT:Cacceptor_loss0.9900
11:119187938:A:AGacceptor_gain0.9900
11:119187938:AG:Aacceptor_loss0.9900
11:119187939:G:Aacceptor_loss0.9900
11:119187939:G:GGacceptor_gain0.9900
11:119187939:GCTTT:Gacceptor_gain0.9900
11:119188145:G:GGdonor_gain0.9900
11:119188147:GA:Gdonor_loss0.9900
11:119188547:GCATG:Gdonor_gain0.9900
11:119188549:ATGG:Adonor_loss0.9900
11:119188550:TGGTG:Tdonor_loss0.9900

AlphaMissense

3218 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:119186545:T:CF128S0.988
11:119186644:T:CI161T0.988
11:119188105:T:CF341L0.987
11:119188107:C:AF341L0.987
11:119188107:C:GF341L0.987
11:119188106:T:CF341S0.986
11:119186544:T:CF128L0.985
11:119186546:C:AF128L0.985
11:119186546:C:GF128L0.985
11:119188429:G:CA379P0.976
11:119188484:T:CI397T0.976
11:119187642:T:AL266Q0.974
11:119186644:T:GI161S0.973
11:119188360:T:CF356L0.973
11:119188362:C:AF356L0.973
11:119188362:C:GF356L0.973
11:119188099:T:CF339L0.972
11:119188101:T:AF339L0.972
11:119188101:T:GF339L0.972
11:119186626:T:AL155H0.971
11:119187609:C:AA255D0.971
11:119187445:T:CF235S0.967
11:119186657:C:AN165K0.965
11:119186657:C:GN165K0.965
11:119187642:T:GL266R0.965
11:119188821:T:CF480S0.965
11:119187654:A:TN270I0.964
11:119187624:T:AV260E0.963
11:119188421:G:CR376P0.963
11:119188406:T:CM371T0.960

dbSNP variants (sampled 300 via entrez): RS1000176398 (11:119190517 T>C), RS1000342609 (11:119187199 G>A,C,T), RS1000373732 (11:119186869 T>C), RS1001735789 (11:119187913 T>C), RS1002403169 (11:119186394 C>A), RS1002887014 (11:119186192 T>C), RS1004474376 (11:119186799 C>T), RS1005149239 (11:119189404 A>G), RS1005181599 (11:119189157 C>A), RS1006188030 (11:119187948 G>A), RS1006494936 (11:119184944 A>C), RS1006668192 (11:119189786 T>A,C), RS1007210060 (11:119185402 C>T), RS1007376318 (11:119188572 G>A), RS1007404323 (11:119188317 A>G)

Disease associations

OMIM: gene MIM:607146 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): congenital portosystemic shunt (MONDO:0018811)

Orphanet (1): Congenital portosystemic shunt (Orphanet:480531)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
propionaldehydedecreases expression1
terbufosdecreases methylation1
sodium arsenitedecreases expression1
butyraldehydedecreases expression1
pentanaldecreases expression1
CGP 52608affects binding, increases reaction1
abrinedecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Acetaminophendecreases expression1
Aldehydesdecreases expression1
Arsenicaffects methylation1
Benzo(a)pyrenedecreases expression1
Fonofosdecreases methylation1
Parathiondecreases methylation1
Plant Extractsdecreases expression, affects cotreatment1
Silicon Dioxidedecreases expression1
Tetrachlorodibenzodioxinincreases expression1
Tobacco Smoke Pollutiondecreases expression1
Palmitic Aciddecreases expression1
Okadaic Aciddecreases expression1

Clinical trials (associated diseases)

2 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT06041906Not specifiedENROLLING_BY_INVITATIONInternational Registry of Congenital Portosystemic Shunt (IRCPSS)
NCT07314814Not specifiedNOT_YET_RECRUITINGGenetic Hallmarks of Patients With Congenital Portosystemic Shunts and Portopulmonary Hypertension
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): congenital portosystemic shunt