FXYD6

gene
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Summary

FXYD6 (FXYD domain containing ion transport regulator 6, HGNC:4030) is a protein-coding gene on chromosome 11q23.3, encoding FXYD domain-containing ion transport regulator 6 (Q9H0Q3). Associates with and regulates the activity of the sodium/potassium-transporting ATPase (NKA) which catalyzes the hydrolysis of ATP coupled with the exchange of Na(+) and K(+) ions across the plasma membrane.

This gene encodes a member of the FXYD family of transmembrane proteins. This particular protein encodes phosphohippolin, which likely affects the activity of Na,K-ATPase. Multiple alternatively spliced transcript variants encoding the same protein have been described. Related pseudogenes have been identified on chromosomes 10 and X. Read-through transcripts have been observed between this locus and the downstream sodium/potassium-transporting ATPase subunit gamma (FXYD2, GeneID 486) locus.

Source: NCBI Gene 53826 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 6 total
  • MANE Select transcript: NM_022003

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4030
Approved symbolFXYD6
NameFXYD domain containing ion transport regulator 6
Location11q23.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000137726
Ensembl biotypeprotein_coding
OMIM606683
Entrez53826

Gene structure

Transcript identifiers

Ensembl transcripts: 63 — 55 protein_coding, 5 retained_intron, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000260282, ENST00000524656, ENST00000524841, ENST00000526014, ENST00000527053, ENST00000527429, ENST00000527717, ENST00000529335, ENST00000530956, ENST00000534125, ENST00000539526, ENST00000540359, ENST00000579486, ENST00000583233, ENST00000583660, ENST00000584230, ENST00000584394, ENST00000902933, ENST00000902934, ENST00000902935, ENST00000902936, ENST00000902937, ENST00000902938, ENST00000902939, ENST00000902940, ENST00000902941, ENST00000902942, ENST00000902943, ENST00000902944, ENST00000902945, ENST00000902946, ENST00000902947, ENST00000902948, ENST00000902949, ENST00000902950, ENST00000902951, ENST00000902952, ENST00000902953, ENST00000902954, ENST00000902955, ENST00000902956, ENST00000902957, ENST00000902958, ENST00000902959, ENST00000902960, ENST00000902961, ENST00000902962, ENST00000912676, ENST00000941139, ENST00000941140, ENST00000941141, ENST00000941142, ENST00000941143, ENST00000941144, ENST00000941145, ENST00000941146, ENST00000941147, ENST00000941148, ENST00000941149, ENST00000941150, ENST00000941151, ENST00000941152, ENST00000941153

RefSeq mRNA: 5 — MANE Select: NM_022003 NM_001164831, NM_001164832, NM_001164836, NM_001164837, NM_022003

CCDS: CCDS8387

Canonical transcript exons

ENST00000526014 — 8 exons

ExonStartEnd
ENSE00001130048117836981117838277
ENSE00002155235117876592117876658
ENSE00003488781117840319117840368
ENSE00003549740117841990117842028
ENSE00003627783117839781117839830
ENSE00003642452117841791117841865
ENSE00003786068117841148117841184
ENSE00003787656117842719117842781

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 99.62.

FANTOM5 (CAGE): breadth broad, TPM avg 11.5342 / max 629.6528, expressed in 717 samples.

FANTOM5 promoters (14 alternative TSS)

Promoter IDTPM avgSamples expressed
12253426.7508727
1225293.5332223
1225302.4702213
1225361.3174373
1225371.2602319
1225350.9594372
1225390.5457183
1225280.501482
1225380.4428150
1225270.198166

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534399.62gold quality
prefrontal cortexUBERON:000045199.46gold quality
ganglionic eminenceUBERON:000402399.45gold quality
ventricular zoneUBERON:000305399.41gold quality
right frontal lobeUBERON:000281099.40gold quality
right hemisphere of cerebellumUBERON:001489099.35gold quality
cerebellar hemisphereUBERON:000224599.32gold quality
cerebellar cortexUBERON:000212999.31gold quality
body of uterusUBERON:000985399.27gold quality
cingulate cortexUBERON:000302799.24gold quality
anterior cingulate cortexUBERON:000983599.24gold quality
frontal cortexUBERON:000187099.23gold quality
frontal lobeUBERON:001652599.23gold quality
dorsolateral prefrontal cortexUBERON:000983499.21gold quality
Brodmann (1909) area 9UBERON:001354099.16gold quality
orbitofrontal cortexUBERON:000416799.12gold quality
neocortexUBERON:000195099.08gold quality
cerebellumUBERON:000203799.07gold quality
left uterine tubeUBERON:000130399.06gold quality
right ovaryUBERON:000211899.05gold quality
left ovaryUBERON:000211999.01gold quality
middle temporal gyrusUBERON:000277198.95gold quality
amygdalaUBERON:000187698.85gold quality
Brodmann (1909) area 46UBERON:000648398.77gold quality
cerebral cortexUBERON:000095698.74gold quality
tendon of biceps brachiiUBERON:000818898.72gold quality
muscle layer of sigmoid colonUBERON:003580598.71gold quality
hypothalamusUBERON:000189898.54gold quality
temporal lobeUBERON:000187198.53gold quality
superior frontal gyrusUBERON:000266198.47gold quality

Single-cell (SCXA)

Detected in 20 experiment(s), a significant marker in 19.

ExperimentMarker?Max mean expression
E-MTAB-10485yes1497.65
E-HCAD-5yes1476.28
E-MTAB-9435yes1411.98
E-ENAD-27yes399.26
E-MTAB-10553yes46.83
E-GEOD-134144yes39.44
E-HCAD-35yes39.44
E-HCAD-10yes36.75
E-MTAB-5061yes28.38
E-GEOD-81547yes25.95
E-HCAD-31yes25.64
E-GEOD-84465yes25.46
E-HCAD-1yes20.03
E-GEOD-81608yes15.92
E-MTAB-6701yes15.10

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

55 targeting FXYD6, 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-8485100.0077.574731
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-449699.8868.892236
HSA-MIR-137-3P99.8774.742401
HSA-MIR-449299.8768.253611
HSA-MIR-6739-5P99.8067.872806
HSA-MIR-6733-5P99.7467.942759
HSA-MIR-1255A99.7468.09744
HSA-MIR-1255B-5P99.7468.16741
HSA-MIR-1212499.6869.172700
HSA-MIR-320299.6667.702737
HSA-MIR-466399.6265.33957
HSA-MIR-426199.5970.303415
HSA-MIR-315399.5567.592337
HSA-MIR-486-3P99.5166.821901
HSA-MIR-608199.4866.071446
HSA-MIR-766-5P99.4767.912225
HSA-MIR-147B-5P99.4570.622432
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-361299.4566.021333
HSA-MIR-65099.4565.771309
HSA-MIR-4652-3P99.3370.022742
HSA-MIR-6828-5P99.3169.211433
HSA-MIR-449B-3P99.2067.241047
HSA-MIR-6852-5P99.1766.692073
HSA-MIR-807799.1766.67862
HSA-MIR-6510-5P99.1466.591081
HSA-MIR-6815-3P99.1368.981530
HSA-MIR-125399.1267.081688

Literature-anchored findings (GeneRIF, showing 9)

  • Base-pair changes in FXYD6 or in associated promoter/control regions are likely to cause abnormal function or expression of phosphohippolin and to increase genetic susceptibility to schizophrenia. (PMID:17357072)
  • Our findings suggest that FXYD6 is unlikely to be related to the development of schizophrenia in a Japanese population. (PMID:18455306)
  • Data show that FXYD6 does not play a role in schizophrenia in the Chinese Han population. (PMID:20149392)
  • these results support that FXYD6 is a susceptibility gene of schizophrenia. (PMID:21216238)
  • FXYD6 gene might play an important role in schizophrenia susceptibility. (PMID:21983730)
  • FXYD6 plays a critical role of in hepatocellular carcinoma disease progression. (PMID:24715268)
  • FXYD6 was verified to be directly interacting with miR-137.. (PMID:26302771)
  • FXYD protein isoforms differentially modulate human Na/K pump function. (PMID:33231612)
  • Identification of FXYD6 as the novel biomarker for glioma based on differential expression and DNA methylation. (PMID:38093622)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriofxyd6ENSDARG00000100971
mus_musculusFxyd6ENSMUSG00000066705
rattus_norvegicusFxyd6ENSRNOG00000016412

Paralogs (6): FXYD5 (ENSG00000089327), FXYD3 (ENSG00000089356), FXYD2 (ENSG00000137731), FXYD4 (ENSG00000150201), FXYD7 (ENSG00000221946), FXYD1 (ENSG00000266964)

Protein

Protein identifiers

FXYD domain-containing ion transport regulator 6Q9H0Q3 (reviewed: Q9H0Q3)

Alternative names: Phosphohippolin

All UniProt accessions (4): E9PHZ3, E9PJ02, Q9H0Q3, J3QKN1

UniProt curated annotations — full annotation on UniProt →

Function. Associates with and regulates the activity of the sodium/potassium-transporting ATPase (NKA) which catalyzes the hydrolysis of ATP coupled with the exchange of Na(+) and K(+) ions across the plasma membrane. Reduces the apparent affinity for intracellular Na(+) with no change in the apparent affinity for extracellular K(+). In addition to modulating NKA kinetics, may also function as a regulator of NKA localization to the plasma membrane.

Subunit / interactions. Regulatory subunit of the sodium/potassium-transporting ATPase which is composed of a catalytic alpha subunit, a non-catalytic beta subunit and an additional regulatory subunit. The regulatory subunit, a member of the FXYD protein family, modulates the enzymatic activity in a tissue- and isoform-specific way by changing affinities of the Na+/K+-ATPase toward Na(+), K(+) or ATP.

Subcellular location. Cell membrane.

Similarity. Belongs to the FXYD family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9H0Q3-11yes
Q9H0Q3-22

RefSeq proteins (5): NP_001158303, NP_001158304, NP_001158308, NP_001158309, NP_071286* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000272Ion-transport_regulator_FXYDFamily
IPR047297FXYD_motifConserved_site

Pfam: PF02038

UniProt features (9 total): topological domain 2, signal peptide 1, chain 1, transmembrane region 1, region of interest 1, splice variant 1, turn 1, helix 1

Structure

Experimental structures (PDB)

5 structures.

PDBMethodResolution (Å)
8D3VELECTRON MICROSCOPY3.4
8D3WELECTRON MICROSCOPY3.5
8D3UELECTRON MICROSCOPY3.7
8D3YELECTRON MICROSCOPY3.9
8D3XELECTRON MICROSCOPY4.1

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H0Q3-F170.350.13

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-5578775Ion homeostasis
R-HSA-936837Ion transport by P-type ATPases
R-HSA-9679191Potential therapeutics for SARS

MSigDB gene sets: 220 (showing top): GOBP_POTASSIUM_ION_TRANSPORT, GNF2_RTN1, GOBP_ESTABLISHMENT_OR_MAINTENANCE_OF_TRANSMEMBRANE_ELECTROCHEMICAL_GRADIENT, GOBP_SODIUM_ION_TRANSMEMBRANE_TRANSPORT, GOBP_POTASSIUM_ION_HOMEOSTASIS, GOBP_POSITIVE_REGULATION_OF_SODIUM_ION_TRANSPORT, GOBP_POSITIVE_REGULATION_OF_TRANSMEMBRANE_TRANSPORT, EFC_Q6, GOBP_MONOATOMIC_CATION_TRANSPORT, GOBP_REGULATION_OF_SODIUM_ION_TRANSPORT, ONKEN_UVEAL_MELANOMA_UP, GOBP_POSITIVE_REGULATION_OF_MONOATOMIC_ION_TRANSPORT, TGCTGAY_UNKNOWN, DELYS_THYROID_CANCER_DN, GOBP_INTRACELLULAR_POTASSIUM_ION_HOMEOSTASIS

GO Biological Process (5): potassium ion transport (GO:0006813), sodium ion transport (GO:0006814), positive regulation of sodium ion export across plasma membrane (GO:1903278), monoatomic ion transport (GO:0006811), regulation of monoatomic ion transport (GO:0043269)

GO Molecular Function (3): sodium channel regulator activity (GO:0017080), protein binding (GO:0005515), ion channel regulator activity (GO:0099106)

GO Cellular Component (5): plasma membrane (GO:0005886), presynaptic membrane (GO:0042734), postsynaptic membrane (GO:0045211), glutamatergic synapse (GO:0098978), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Cardiac conduction1
Ion channel transport1
SARS-CoV Infections1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
metal ion transport2
synaptic membrane2
sodium ion export across plasma membrane1
positive regulation of sodium ion transmembrane transport1
regulation of sodium ion export across plasma membrane1
transport1
monoatomic ion transport1
regulation of transport1
sodium channel activity1
ion channel regulator activity1
binding1
monoatomic ion channel activity1
channel regulator activity1
membrane1
cell periphery1
presynapse1
postsynapse1
synapse1
cellular anatomical structure1

Protein interactions and networks

STRING

658 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FXYD6FXYD5Q96DB9729
FXYD6DRD2P14416588
FXYD6TYRP14679549
FXYD6EXOC1LA0A1B0GW35401
FXYD6MPZL3Q6UWV2355
FXYD6ITPRIPL2Q3MIP1353
FXYD6GPR68Q15743353
FXYD6KCNS1Q96KK3353
FXYD6SULF2Q8IWU5351
FXYD6LXNQ9BS40350
FXYD6LDB2O43679350
FXYD6COL13A1Q5TAT6350
FXYD6PANX1Q96RD7349
FXYD6CRIM1Q9NZV1347
FXYD6HOATZQ6PI97325

IntAct

189 interactions, top by confidence:

ABTypeScore
FXYD6CREB3L1psi-mi:“MI:0915”(physical association)0.720
CREB3L1FXYD6psi-mi:“MI:0915”(physical association)0.720
SVOPFXYD6psi-mi:“MI:0915”(physical association)0.600
FXYD6LHFPL5psi-mi:“MI:0915”(physical association)0.560
FXYD6psi-mi:“MI:0915”(physical association)0.560
FXYD6FFAR2psi-mi:“MI:0915”(physical association)0.560
FXYD6RNASEKpsi-mi:“MI:0915”(physical association)0.560
FXYD6SLC35E3psi-mi:“MI:0915”(physical association)0.560
MFFFXYD6psi-mi:“MI:0915”(physical association)0.560
CD74FXYD6psi-mi:“MI:0915”(physical association)0.560
SLC30A2FXYD6psi-mi:“MI:0915”(physical association)0.560
SLC47A1FXYD6psi-mi:“MI:0915”(physical association)0.560
TMEM237FXYD6psi-mi:“MI:0915”(physical association)0.560
DERL2FXYD6psi-mi:“MI:0915”(physical association)0.560
APCDD1LFXYD6psi-mi:“MI:0915”(physical association)0.560
FXYD6psi-mi:“MI:0915”(physical association)0.560
RHBDL1FXYD6psi-mi:“MI:0915”(physical association)0.560
CLEC10AFXYD6psi-mi:“MI:0915”(physical association)0.560
FXYD6CERS4psi-mi:“MI:0915”(physical association)0.560
ELOVL4FXYD6psi-mi:“MI:0915”(physical association)0.560
TM4SF18FXYD6psi-mi:“MI:0915”(physical association)0.560
TMEM35AFXYD6psi-mi:“MI:0915”(physical association)0.560

BioGRID (124): CREB3L1 (Two-hybrid), FXYD6 (Two-hybrid), FXYD6 (Affinity Capture-MS), FXYD6 (Affinity Capture-MS), FXYD6 (Two-hybrid), FXYD6 (Two-hybrid), HAUS2 (Two-hybrid), CCDC90B (Two-hybrid), TRIM27 (Two-hybrid), SLC35E1 (Two-hybrid), FXYD6 (Two-hybrid), FXYD6 (Two-hybrid), FXYD6-FXYD2 (Two-hybrid), FXYD6 (Two-hybrid), FXYD6 (Two-hybrid)

ESM2 similar proteins: A0A1B0GW64, A2AFR3, A4IFL2, A6QLZ5, A8MVS5, A8MWV9, E1BBQ2, E9Q2Z6, O54693, O73612, P01134, P0C8R9, P18519, P48030, P52795, P52796, P98172, Q0VAQ4, Q0VBP7, Q14CM0, Q15223, Q3MHZ5, Q4FZH1, Q4R566, Q5JRV8, Q5R8M2, Q5RB29, Q5T1S8, Q5T292, Q5VX71, Q6AYP5, Q7TPF1, Q8BHW5, Q8BR63, Q8CA71, Q8IVY1, Q8R5M8, Q91WM6, Q91XV6, Q96DD7

Diamond homologs: C0HJJ0, P58550, Q3MHZ5, Q3SZX0, Q4R566, Q5RB29, Q63113, Q91XV6, Q9D164, Q9D2W0, Q9H0Q3, W5P3P0, G1TZA0, I3LMB3, O00168, O08589, O13001, O97797, P54710, P56513, P58549, P59645, P59646, P59647, P59648, P59649, Q04645, Q04646, Q04679, Q04680, Q14802, Q3ZBJ3, Q61835, Q96DB9, Q9Z239, P97808

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance6
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1565 predictions. Top by Δscore:

VariantEffectΔscore
11:117839826:TGTTG:Tacceptor_gain1.0000
11:117839831:C:CCacceptor_gain1.0000
11:117840252:T:TAdonor_gain1.0000
11:117840366:GCC:Gacceptor_gain1.0000
11:117840367:CC:Cacceptor_gain1.0000
11:117840367:CCC:Cacceptor_gain1.0000
11:117840368:CC:Cacceptor_gain1.0000
11:117841787:TTA:Tdonor_loss1.0000
11:117841788:TACTT:Tdonor_loss1.0000
11:117841789:A:ACdonor_gain1.0000
11:117841789:A:Tdonor_loss1.0000
11:117841790:C:CGdonor_gain1.0000
11:117841790:CT:Cdonor_gain1.0000
11:117841790:CTT:Cdonor_gain1.0000
11:117841790:CTTA:Cdonor_gain1.0000
11:117841793:A:ACdonor_gain1.0000
11:117841863:AATC:Aacceptor_loss1.0000
11:117841864:ATC:Aacceptor_loss1.0000
11:117841865:TC:Tacceptor_loss1.0000
11:117841865:TCTG:Tacceptor_loss1.0000
11:117841866:C:CCacceptor_gain1.0000
11:117841866:C:CGacceptor_loss1.0000
11:117841986:TCACC:Tdonor_loss1.0000
11:117841987:CA:Cdonor_loss1.0000
11:117841988:A:ATdonor_loss1.0000
11:117842026:CTG:Cacceptor_gain1.0000
11:117842027:TG:Tacceptor_gain1.0000
11:117842029:C:CCacceptor_gain1.0000
11:117842713:ACTT:Adonor_loss1.0000
11:117842714:CTT:Cdonor_loss1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000051671 (11:117847999 A>G), RS1000121950 (11:117855038 T>A), RS1000227894 (11:117838249 G>A,C), RS1000270864 (11:117876994 G>T), RS1000367387 (11:117866249 C>T), RS1000410324 (11:117855345 C>G,T), RS1000416177 (11:117860321 A>C,G), RS1000511273 (11:117870805 C>T), RS1000539118 (11:117837205 C>G,T), RS1000761057 (11:117870669 G>A), RS1000864361 (11:117859211 T>A,C,G), RS1000883777 (11:117865954 C>G,T), RS1000884798 (11:117841984 G>A,T), RS1000942489 (11:117848295 G>A), RS1001008289 (11:117836898 C>A,T)

Disease associations

OMIM: gene MIM:606683 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST003997_18Myopia1.000000e-11
GCST006993_11Hippocampal volume in Alzheimer’s disease dementia1.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0005035hippocampal volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression3
Decitabineaffects expression, affects cotreatment2
Nickeldecreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
TL8-506increases expression, affects cotreatment1
methylmercuric chloridedecreases expression1
pirinixic acidaffects binding, decreases expression, increases activity1
beta-lapachonedecreases expression1
sodium arseniteaffects methylation1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, affects cotreatment1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
gardiquimodincreases expression, decreases reaction1
Vorinostataffects expression, affects cotreatment1
Benzo(a)pyreneaffects methylation, increases methylation1
Carbamazepineaffects expression1
Cisplatinaffects expression1
Doxorubicindecreases expression1
Leadaffects expression1
Lipopolysaccharidesincreases expression, affects response to substance, affects cotreatment1
Poly I-Caffects cotreatment, increases expression1
Silicon Dioxidedecreases expression1
Dronabinolincreases expression1
Thimerosaldecreases expression1
Tunicamycindecreases expression1
Vitamin Eincreases expression1
Aflatoxin B1increases methylation1
Asbestos, Crocidolitedecreases methylation1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.