PLEKHF2

gene
On this page

Also known as ZFYVE18PHAFIN2FLJ13187

Summary

PLEKHF2 (pleckstrin homology and FYVE domain containing 2, HGNC:20757) is a protein-coding gene on chromosome 8q22.1, encoding Pleckstrin homology domain-containing family F member 2 (Q9H8W4). May play a role in early endosome fusion upstream of RAB5, hence regulating receptor trafficking and fluid-phase transport.

Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in endosome organization and endosome to lysosome transport. Located in transport vesicle.

Source: NCBI Gene 79666 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 14 total
  • MANE Select transcript: NM_024613

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20757
Approved symbolPLEKHF2
Namepleckstrin homology and FYVE domain containing 2
Location8q22.1
Locus typegene with protein product
StatusApproved
AliasesZFYVE18, PHAFIN2, FLJ13187
Ensembl geneENSG00000175895
Ensembl biotypeprotein_coding
OMIM615208
Entrez79666

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 8 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000315367, ENST00000519516, ENST00000700745, ENST00000700746, ENST00000700747, ENST00000700748, ENST00000700749, ENST00000908157, ENST00000945912

RefSeq mRNA: 1 — MANE Select: NM_024613 NM_024613

CCDS: CCDS6267

Canonical transcript exons

ENST00000315367 — 2 exons

ExonStartEnd
ENSE000039807209515403195156685
ENSE000039807279513378595134030

Expression profiles

Bgee: expression breadth ubiquitous, 268 present calls, max score 97.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.6285 / max 461.4001, expressed in 1800 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
898199.45301710
898226.61491165
898213.61101149
898201.8990807
898231.3582605
898180.6924328

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065597.44gold quality
oocyteCL:000002395.14gold quality
upper leg skinUBERON:000426294.28gold quality
palpebral conjunctivaUBERON:000181294.21gold quality
bronchial epithelial cellCL:000232894.01gold quality
skin of hipUBERON:000155493.06gold quality
monocyteCL:000057692.89gold quality
mononuclear cellCL:000084292.87gold quality
leukocyteCL:000073892.73gold quality
spermCL:000001992.51gold quality
bone marrowUBERON:000237192.31gold quality
corpus epididymisUBERON:000435991.81gold quality
epithelium of bronchusUBERON:000203191.34gold quality
olfactory segment of nasal mucosaUBERON:000538691.22gold quality
epithelium of nasopharynxUBERON:000195191.16gold quality
mucosa of sigmoid colonUBERON:000499391.14gold quality
caput epididymisUBERON:000435891.09gold quality
colonic mucosaUBERON:000031790.86gold quality
bronchusUBERON:000218590.58gold quality
lymph nodeUBERON:000002990.29gold quality
islet of LangerhansUBERON:000000690.05gold quality
mucosa of paranasal sinusUBERON:000503090.03gold quality
nasal cavity mucosaUBERON:000182689.60gold quality
trabecular bone tissueUBERON:000248389.54gold quality
vermiform appendixUBERON:000115489.48gold quality
oral cavityUBERON:000016789.43gold quality
amniotic fluidUBERON:000017389.25gold quality
male germ cellCL:000001588.84gold quality
bone marrow cellCL:000209288.71gold quality
superficial temporal arteryUBERON:000161488.05gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1

miRNA regulators (miRDB)

181 targeting PLEKHF2, 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-6740-5P100.0065.64932
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3924100.0072.092394
HSA-MIR-3163100.0077.238605
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-4692100.0067.322066
HSA-MIR-4481100.0066.421669
HSA-MIR-574-5P100.0066.01989
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-548AW99.9972.573559
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-428299.9975.366408
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-60799.9773.625593
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-314899.9775.066478
HSA-MIR-1468-3P99.9672.743797

Literature-anchored findings (GeneRIF, showing 8)

  • Results demonstrate that EAPF/Phafin-2 facilitates TNF-alpha-induced cellular apoptosis through an ER-mitochondrial apoptotic pathway. (PMID:18288467)
  • These results provide a vivid example that an endosome modulator, such as Phafin2, may control the cells’ responses to the extracellular cues. (PMID:19995552)
  • Phafin2 controls EGFR trafficking through early endosomes by facilitating endosome fusion in concert with EEA1. (PMID:22816767)
  • These findings establish that lysosomal accumulation of Akt and Phafin2 is a critical step in the induction of autophagy via an interaction with phosphatidylinositol 3 phosphate. (PMID:24416124)
  • PtdIns(3)P binding to Phafin2 occurs with high affinity, triggering minor conformational changes in the protein. Taken together, these studies represent a platform for establishing the structural basis of Phafin2 molecular interactions and the role of the two potentially redundant PtdIns(3)P-binding domains of the protein in endomembrane compartments. (PMID:28152563)
  • The C-terminal acidic motif of Phafin2 inhibits PH domain binding to phosphatidylinositol 3-phosphate. (PMID:32126233)
  • Bioinformatics analysis of the genes involved in the extension of prostate cancer to adjacent lymph nodes by supervised and unsupervised machine learning methods: The role of SPAG1 and PLEKHF2. (PMID:32619574)
  • The phosphoinositide coincidence detector Phafin2 promotes macropinocytosis by coordinating actin organisation at forming macropinosomes. (PMID:34772942)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioplekhf2ENSDARG00000021141
mus_musculusPlekhf2ENSMUSG00000049969
rattus_norvegicusPlekhf2ENSRNOG00000026662
drosophila_melanogasterrushFBGN0025381
caenorhabditis_elegansWBGENE00014019

Paralogs (13): RUFY3 (ENSG00000018189), ZFYVE16 (ENSG00000039319), SNX29 (ENSG00000048471), ZFYVE26 (ENSG00000072121), RUNDC3B (ENSG00000105784), RUNDC3A (ENSG00000108309), PLEKHM2 (ENSG00000116786), ZFYVE28 (ENSG00000159733), ZFYVE1 (ENSG00000165861), ZFYVE19 (ENSG00000166140), PLEKHF1 (ENSG00000166289), RUFY1 (ENSG00000176783), RUFY2 (ENSG00000204130)

Protein

Protein identifiers

Pleckstrin homology domain-containing family F member 2Q9H8W4 (reviewed: Q9H8W4)

Alternative names: Endoplasmic reticulum-associated apoptosis-involved protein containing PH and FYVE domains, PH and FYVE domain-containing protein 2, Phafin-2, Zinc finger FYVE domain-containing protein 18

All UniProt accessions (1): Q9H8W4

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in early endosome fusion upstream of RAB5, hence regulating receptor trafficking and fluid-phase transport. Enhances cellular sensitivity to TNF-induced apoptosis.

Subunit / interactions. May interact with EEA1.

Subcellular location. Early endosome membrane. Endoplasmic reticulum.

Tissue specificity. Expressed in placenta, ovary and small intestine, as well as in heart and pancreas. Also expressed in peripheral blood mononuclear cells and dendritic cells.

Domain organisation. The PH and FYVE domains may be important for TNF-induced localization to the endoplasmic reticulum and for enhanced cellular sensitivity to TNF-induced apoptosis. The FYVE domain is important for binding to the endosomal membrane.

Induction. Up-regulated by TNF, bacterial lipopolysaccharides (LPS) and phorbol myristate acetate (PMA) (at protein level).

RefSeq proteins (1): NP_078889* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000306Znf_FYVEDomain
IPR001849PH_domainDomain
IPR011011Znf_FYVE_PHDHomologous_superfamily
IPR011993PH-like_dom_sfHomologous_superfamily
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily
IPR017455Znf_FYVE-relDomain
IPR037871PH_PhafinDomain
IPR047966PLEKHF2_FYVEDomain
IPR051765PH_domain-containing_FFamily

Pfam: PF00169, PF01363

UniProt features (18 total): binding site 8, modified residue 4, compositionally biased region 2, chain 1, domain 1, zinc finger region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H8W4-F187.360.78

Functional residue map

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

Ligand- & substrate-binding residues (8): 183; 186; 204; 207; 158; 161; 175; 178

Post-translational modifications (4): 16, 44, 239, 248

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 259 (showing top): GOBP_LYSOSOMAL_TRANSPORT, GOBP_ENDOSOME_ORGANIZATION, MODULE_255, GOBP_VESICLE_ORGANIZATION, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GOBP_ENDOSOME_TO_LYSOSOME_TRANSPORT, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, MODULE_317, GOBP_VACUOLAR_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, PATIL_LIVER_CANCER, MODULE_331, ONKEN_UVEAL_MELANOMA_UP, FOSTER_TOLERANT_MACROPHAGE_UP, SMID_BREAST_CANCER_LUMINAL_B_UP

GO Biological Process (3): endosome organization (GO:0007032), endosome to lysosome transport (GO:0008333), protein transport (GO:0015031)

GO Molecular Function (4): zinc ion binding (GO:0008270), phosphatidylinositol binding (GO:0035091), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (8): early endosome (GO:0005769), endoplasmic reticulum (GO:0005783), transport vesicle (GO:0030133), early endosome membrane (GO:0031901), endosome (GO:0005768), endomembrane system (GO:0012505), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
endomembrane system3
cytoplasm2
cytoplasmic vesicle2
cellular anatomical structure2
endomembrane system organization1
vesicle organization1
lysosomal transport1
intercellular transport1
vesicle-mediated transport1
transport1
intracellular protein localization1
establishment of protein localization1
transition metal ion binding1
anion binding1
binding1
cation binding1
endosome1
intracellular membrane-bounded organelle1
early endosome1
endosome membrane1
vacuole1
plasma membrane1
intracellular vesicle1

Protein interactions and networks

STRING

584 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PLEKHF2AKT1P31749571
PLEKHF2PIKFYVEQ9Y2I7454
PLEKHF2SNX29Q8TEQ0410
PLEKHF2PLEKHG1Q9ULL1410
PLEKHF2NOP53Q9NZM5379
PLEKHF2FAM43AQ8N2R8379
PLEKHF2VRK2Q86Y07375
PLEKHF2INO80EQ8NBZ0350
PLEKHF2PLEK2Q9NYT0349
PLEKHF2PLEKP08567348
PLEKHF2PHIPQ8WWQ0335
PLEKHF2MED4Q9NPJ6333
PLEKHF2PHF5AQ7RTV0332
PLEKHF2CYRIAQ9H0Q0324
PLEKHF2ZNF592Q92610323

IntAct

516 interactions, top by confidence:

ABTypeScore
PLEKHF2FRMD8psi-mi:“MI:0915”(physical association)0.720
FBXO28PLEKHF2psi-mi:“MI:0915”(physical association)0.720
HSPB7PLEKHF2psi-mi:“MI:0915”(physical association)0.720
FRMD8PLEKHF2psi-mi:“MI:0915”(physical association)0.720
PLEKHF2FBXO28psi-mi:“MI:0915”(physical association)0.720
MEAF6PLEKHF2psi-mi:“MI:0915”(physical association)0.700
PLEKHF2MEAF6psi-mi:“MI:0915”(physical association)0.700
PLEKHF2LDOC1psi-mi:“MI:0915”(physical association)0.700
PLEKHF2TNFAIP8psi-mi:“MI:0915”(physical association)0.670
ACY3PLEKHF2psi-mi:“MI:0915”(physical association)0.670
PLEKHF2ACY3psi-mi:“MI:0915”(physical association)0.670
BLOC1S6PLEKHF2psi-mi:“MI:0915”(physical association)0.670
RABAC1PLEKHF2psi-mi:“MI:0915”(physical association)0.620
CHIC2PLEKHF2psi-mi:“MI:0915”(physical association)0.620
MBIPPLEKHF2psi-mi:“MI:0915”(physical association)0.620

BioGRID (224): PLEKHF2 (Two-hybrid), PLEKHF2 (Two-hybrid), PLEKHF2 (Two-hybrid), PLEKHF2 (Two-hybrid), PLEKHF2 (Two-hybrid), PLEKHF2 (Two-hybrid), PLEKHF2 (Two-hybrid), PLEKHF2 (Two-hybrid), PLEKHF2 (Two-hybrid), PLEKHF2 (Two-hybrid), PLEKHF2 (Two-hybrid), PLEKHF2 (Two-hybrid), PLEKHF2 (Two-hybrid), PLEKHF2 (Two-hybrid), PLEKHF2 (Two-hybrid)

ESM2 similar proteins: A2ALK8, A7MB43, D3ZDI6, F1LYQ8, F1P065, F8VPU2, O08967, O43739, O94887, P12264, P26045, P29074, P52735, P59113, P63034, P63035, P97694, P97696, Q0IJ35, Q15438, Q28013, Q2KI41, Q32NH8, Q5R8M5, Q5RAB8, Q5RID7, Q5ZLY5, Q60992, Q6TEM9, Q76MY7, Q76MZ1, Q7ZUV1, Q80YW0, Q8BM54, Q8WY64, Q91VS8, Q91WB4, Q925E0, Q93646, Q96QG7

Diamond homologs: A0A0D1E015, A0JMD2, A1CEK1, A1DFP5, A2QWA2, A4QTV1, A8QCE4, A8XJZ8, B0G126, B0WAQ0, B3MT31, B3P851, B4G2G5, B4IC49, B4JHI7, B4K982, B4M140, B4NFJ7, B4PRU6, D2H5P6, D3ZVP7, D4A8G9, E1BLZ4, F1MM41, F7EP40, O13821, O14964, O59722, O76902, O95405, O96838, P0CS26, P0CS27, P34756, P40343, Q05B78, Q08CN9, Q0CJV3, Q0P4S0, Q0U4Z8

SIGNOR signaling

1 interactions.

AEffectBMechanism
PLEKHF2“up-regulates activity”EEA1binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance14
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

355 predictions. Top by Δscore:

VariantEffectΔscore
8:95154026:AAAAG:Aacceptor_gain1.0000
8:95154029:A:Gacceptor_gain1.0000
8:95134027:CGGG:Cdonor_loss0.9900
8:95134028:GGG:Gdonor_gain0.9900
8:95134029:GG:Gdonor_gain0.9900
8:95134029:GGG:Gdonor_gain0.9900
8:95134030:GG:Gdonor_gain0.9900
8:95134031:G:GGdonor_gain0.9900
8:95134032:T:Gdonor_loss0.9900
8:95154026:A:AGacceptor_gain0.9900
8:95154027:A:Gacceptor_gain0.9900
8:95154027:AAAG:Aacceptor_gain0.9900
8:95154028:A:Gacceptor_gain0.9900
8:95154028:AAG:Aacceptor_gain0.9900
8:95154029:A:ACacceptor_loss0.9900
8:95154030:G:GGacceptor_gain0.9900
8:95154030:G:GTacceptor_loss0.9900
8:95154030:GGCT:Gacceptor_gain0.9900
8:95154029:AG:Aacceptor_gain0.9800
8:95154030:GG:Gacceptor_gain0.9800
8:95154030:GGC:Gacceptor_gain0.9800
8:95154030:GGCTA:Gacceptor_gain0.9800
8:95133976:G:GTdonor_gain0.9600
8:95134026:TCGGG:Tdonor_gain0.9600
8:95148010:A:Gdonor_gain0.9500
8:95151961:A:Gdonor_gain0.9400
8:95153204:G:GTdonor_gain0.9300
8:95134036:TG:Tdonor_gain0.9100
8:95156472:AATAT:Aacceptor_gain0.9100
8:95134027:CGGGG:Cdonor_gain0.9000

AlphaMissense

1659 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:95154108:T:CF22L1.000
8:95154109:T:CF22S1.000
8:95154110:T:AF22L1.000
8:95154110:T:GF22L1.000
8:95154130:T:CL29S1.000
8:95154145:G:CR34P1.000
8:95154151:T:CL36P1.000
8:95154157:G:AG38E1.000
8:95154162:G:AG40R1.000
8:95154162:G:CG40R1.000
8:95154163:G:AG40E1.000
8:95154163:G:TG40V1.000
8:95154169:T:CL42S1.000
8:95154169:T:GL42W1.000
8:95154174:A:CK44Q1.000
8:95154174:A:GK44E1.000
8:95154176:G:CK44N1.000
8:95154176:G:TK44N1.000
8:95154180:T:CC46R1.000
8:95154181:G:AC46Y1.000
8:95154184:G:CR47T1.000
8:95154184:G:TR47M1.000
8:95154185:G:CR47S1.000
8:95154185:G:TR47S1.000
8:95154202:G:CR53T1.000
8:95154202:G:TR53M1.000
8:95154203:G:CR53S1.000
8:95154203:G:TR53S1.000
8:95154208:T:CF55S1.000
8:95154210:T:CF56L1.000

dbSNP variants (sampled 300 via entrez): RS1000352980 (8:95138720 A>G), RS1000416897 (8:95152636 G>A), RS1000465072 (8:95147628 T>C,G), RS1000519722 (8:95133831 G>A), RS1000612339 (8:95148199 GT>G,GTT), RS1000718757 (8:95133711 G>T), RS1000769868 (8:95135096 C>A), RS1000837769 (8:95155184 T>C), RS1000844907 (8:95146974 A>G), RS1000908296 (8:95141859 C>T), RS1000956719 (8:95140303 A>C,G), RS1001028568 (8:95154967 C>T), RS1001184232 (8:95152184 G>A), RS1001215403 (8:95151775 A>C), RS1001324664 (8:95136364 A>G)

Disease associations

OMIM: gene MIM:615208 | disease phenotypes: MIM:118100, MIM:613094, MIM:613703, MIM:615360

GenCC curated gene-disease

Mondo (4): Klippel-Feil syndrome 1, autosomal dominant (MONDO:0007306), isolated microphthalmia 4 (MONDO:0013130), microphthalmia, isolated, with coloboma 6 (MONDO:0013376), Leber congenital amaurosis 17 (MONDO:0014145)

Orphanet (4): Isolated Klippel-Feil syndrome (Orphanet:2345), Isolated microphthalmia-anophthalmia-coloboma (Orphanet:2542), Leber congenital amaurosis (Orphanet:65), Colobomatous microphthalmia (Orphanet:98938)

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST000823_8Radiation response8.000000e-06
GCST000823_9Radiation response4.000000e-07

MeSH disease descriptors (2)

DescriptorNameTree numbers
C536887Klippel Feil syndrome dominant type (supp.)
C567757Microphthalmia, Isolated 4 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression4
Estradioldecreases expression3
Air Pollutantsincreases abundance, decreases expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
FR900359affects phosphorylation1
dicrotophosdecreases expression1
bisphenol Adecreases expression1
trichostatin Aincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
sodium arseniteincreases expression1
cobaltous chlorideincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
abrineincreases expression1
dorsomorphinaffects cotreatment, increases expression1
Resveratrolaffects cotreatment, decreases expression1
Fulvestrantincreases expression1
Vorinostatincreases expression1
Leflunomideincreases expression1
Acetaminophenincreases expression1
Benzo(a)pyrenedecreases methylation1
Cisplatinincreases expression1
Coalincreases abundance, decreases expression1
Coumestrolaffects cotreatment, decreases expression1
Diethylstilbestroldecreases expression1
Golddecreases expression1
Hexestroldecreases expression1
Mestranoldecreases expression1
Smokedecreases expression, increases abundance1
Thimerosalincreases expression, affects cotreatment1
Thiramincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03741790Not specifiedACTIVE_NOT_RECRUITINGAirway Management of Pediatric Patients With Klippel-Feil Syndrome
NCT06489392Not specifiedCOMPLETEDMehri Turki Webbed Neck Classification