EFR3B

gene
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Also known as FLJ37871

Summary

EFR3B (EFR3 homolog B, HGNC:29155) is a protein-coding gene on chromosome 2p23.3, encoding Protein EFR3 homolog B (Q9Y2G0). Component of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane.

Involved in phosphatidylinositol phosphate biosynthetic process and protein localization to plasma membrane. Located in actin cytoskeleton; cytosol; and plasma membrane.

Source: NCBI Gene 22979 — RefSeq curated summary.

At a glance

  • GWAS associations: 31
  • Clinical variants (ClinVar): 80 total — 1 pathogenic
  • MANE Select transcript: NM_014971

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29155
Approved symbolEFR3B
NameEFR3 homolog B
Location2p23.3
Locus typegene with protein product
StatusApproved
AliasesFLJ37871
Ensembl geneENSG00000084710
Ensembl biotypeprotein_coding
OMIM616797
Entrez22979

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000264719, ENST00000401432, ENST00000402191, ENST00000403714, ENST00000405108, ENST00000858649, ENST00000858650

RefSeq mRNA: 2 — MANE Select: NM_014971 NM_001319099, NM_014971

CCDS: CCDS46231, CCDS82425

Canonical transcript exons

ENST00000403714 — 23 exons

ExonStartEnd
ENSE000007270752512818325128332
ENSE000007270932514136625141433
ENSE000007271002513905925139190
ENSE000007271092513734125137502
ENSE000007271172513652325136598
ENSE000007271382513338325133434
ENSE000007271452513290325133014
ENSE000007271522513175025131911
ENSE000007271662513055225130630
ENSE000007271722512997525130109
ENSE000008089112513136825131503
ENSE000009323182514373525143862
ENSE000009629402513546725135639
ENSE000013314172515371225153761
ENSE000013314202515191425152020
ENSE000013314212514969425149742
ENSE000013314492514496025145051
ENSE000016459042510363725103787
ENSE000026167842515423525159135
ENSE000034797432509132525091401
ENSE000035684622512167325121794
ENSE000035961062509300325093130
ENSE000038447502504207625042319

Expression profiles

Bgee: expression breadth ubiquitous, 199 present calls, max score 96.35.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.5032 / max 217.0966, expressed in 939 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
192065.2797738
192091.2505473
192101.0543450
192070.6604336
192080.132272
192050.126171

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ponsUBERON:000098896.35gold quality
superior vestibular nucleusUBERON:000722795.00gold quality
pigmented layer of retinaUBERON:000178294.51gold quality
retinaUBERON:000096694.49gold quality
cortical plateUBERON:000534391.53gold quality
substantia nigra pars reticulataUBERON:000196691.46gold quality
middle temporal gyrusUBERON:000277191.13gold quality
lateral nuclear group of thalamusUBERON:000273690.75gold quality
entorhinal cortexUBERON:000272890.58gold quality
caudate nucleusUBERON:000187390.37gold quality
Brodmann (1909) area 23UBERON:001355490.24gold quality
substantia nigra pars compactaUBERON:000196590.13gold quality
putamenUBERON:000187490.02gold quality
subthalamic nucleusUBERON:000190689.40gold quality
ventral tegmental areaUBERON:000269189.38gold quality
nucleus accumbensUBERON:000188289.25gold quality
parietal lobeUBERON:000187288.99gold quality
superior frontal gyrusUBERON:000266188.76gold quality
postcentral gyrusUBERON:000258188.70gold quality
medial globus pallidusUBERON:000247788.55gold quality
inferior vagus X ganglionUBERON:000536388.43gold quality
right hemisphere of cerebellumUBERON:001489088.43gold quality
cerebellar cortexUBERON:000212988.18gold quality
cerebellar hemisphereUBERON:000224588.15gold quality
temporal lobeUBERON:000187188.02gold quality
right frontal lobeUBERON:000281088.02gold quality
globus pallidusUBERON:000187588.00gold quality
cerebellumUBERON:000203787.63gold quality
telencephalonUBERON:000189387.60gold quality
Ammon’s hornUBERON:000195487.51gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-6678no2.41
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

195 targeting EFR3B, 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-3613-3P100.0076.367965
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-25-3P99.9874.601817
HSA-MIR-32-5P99.9875.211964
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-807599.9767.20962
HSA-MIR-426799.9666.532368
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-314399.9371.963104
HSA-MIR-22-3P99.9368.13917
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-3681-3P99.8870.462254
HSA-MIR-806799.8669.592260

Literature-anchored findings (GeneRIF, showing 1)

  • These data suggest that mammalian Efr3s contribute to the control of the phosphorylation state and, hence, desensitization of AT1a receptors, and could affect responsiveness of G-protein-coupled receptors in higher eukaryotes. (PMID:25380825)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioefr3baENSDARG00000033516
danio_rerioefr3bbENSDARG00000069318
mus_musculusEfr3bENSMUSG00000020658
rattus_norvegicusEfr3bENSRNOG00000012950
drosophila_melanogasterstmAFBGN0086784
caenorhabditis_elegansWBGENE00016311

Paralogs (1): EFR3A (ENSG00000132294)

Protein

Protein identifiers

Protein EFR3 homolog BQ9Y2G0 (reviewed: Q9Y2G0)

All UniProt accessions (3): Q9Y2G0, E7ESK9, H7BXG9

UniProt curated annotations — full annotation on UniProt →

Function. Component of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane. The complex acts as a regulator of phosphatidylinositol 4-phosphate (PtdIns(4)P) synthesis. In the complex, EFR3B probably acts as the membrane-anchoring component. Also involved in responsiveness to G-protein-coupled receptors; it is however unclear whether this role is direct or indirect.

Subunit / interactions. Component of a phosphatidylinositol 4-kinase (PI4K) complex, composed of PI4KA, EFR3 (EFR3A or EFR3B), TTC7 (TTC7A or TTC7B) and HYCC (HYCC1 or HYCC2).

Subcellular location. Cell membrane. Cytoplasm. Cytosol.

Post-translational modifications. Palmitoylated at its N-terminus, anchoring the protein to the plasma membrane.

Similarity. Belongs to the EFR3 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9Y2G0-11yes
Q9Y2G0-22
Q9Y2G0-33

RefSeq proteins (2): NP_001306028, NP_055786* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR011989ARM-likeHomologous_superfamily
IPR016024ARM-type_foldHomologous_superfamily
IPR049152EFR3-like_ARMRepeat
IPR051851EFR3_HomologsFamily

Pfam: PF21052

UniProt features (7 total): modified residue 3, splice variant 2, chain 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y2G0-F182.080.51

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 (3): 212, 214, 216

Mutagenesis-validated functional residues (1):

PositionPhenotype
5–8induces localization to the cytosol.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 98 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLINOSITOL_METABOLIC_PROCESS, GOBP_BEHAVIOR, BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, GOBP_BIOLOGICAL_PROCESS_INVOLVED_IN_INTRASPECIES_INTERACTION_BETWEEN_ORGANISMS, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_LIPID_BIOSYNTHETIC_PROCESS, GOBP_LOCALIZATION_WITHIN_MEMBRANE

GO Biological Process (4): transmission of nerve impulse (GO:0019226), social behavior (GO:0035176), phosphatidylinositol phosphate biosynthetic process (GO:0046854), protein localization to plasma membrane (GO:0072659)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (5): cytosol (GO:0005829), plasma membrane (GO:0005886), actin cytoskeleton (GO:0015629), cytoplasm (GO:0005737), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
action potential1
cell communication1
chemical synaptic transmission1
nervous system process1
behavior1
biological process involved in intraspecies interaction between organisms1
glycerophospholipid biosynthetic process1
protein localization to membrane1
protein localization to cell periphery1
binding1
cytoplasm1
membrane1
cell periphery1
cytoskeleton1
intracellular anatomical structure1

Protein interactions and networks

STRING

814 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EFR3BTTC7BQ86TV6875
EFR3BTTC7AQ9ULT0768
EFR3BPI4KAP42356713
EFR3BHYCC1Q9BYI3703
EFR3BTMEM150AQ86TG1636
EFR3BHYCC2Q8IXS8588
EFR3BPI4KBP78405488
EFR3BKATNAL2Q8IYT4433
EFR3BRHEXQ6ZWK4431
EFR3BGRAMD1CQ8IYS0421
EFR3BNUGGCQ68CJ6420
EFR3BTMEM205Q6UW68412
EFR3BWDR17Q8IZU2395
EFR3BWDR27A2RRH5380
EFR3BMSLNLQ96KJ4378

IntAct

20 interactions, top by confidence:

ABTypeScore
KCNJ2KCNJ18psi-mi:“MI:2364”(proximity)0.660
RNASE3GGPS1psi-mi:“MI:0914”(association)0.640
SLC16A3CASKpsi-mi:“MI:0914”(association)0.590
HOXB5VPS37Cpsi-mi:“MI:0914”(association)0.530
TIGD5P4HA2psi-mi:“MI:0914”(association)0.530
TMEM185ATSPAN6psi-mi:“MI:0914”(association)0.530
NRASESYT2psi-mi:“MI:2364”(proximity)0.480
FCAREFR3Bpsi-mi:“MI:0915”(physical association)0.400
PI4KAEFR3Apsi-mi:“MI:0914”(association)0.350
S100A2PLEKHG3psi-mi:“MI:0914”(association)0.350
S100A6VWA8psi-mi:“MI:0914”(association)0.350
CENPMDNM1Lpsi-mi:“MI:0914”(association)0.350
MATCAP2PRKAR2Bpsi-mi:“MI:0914”(association)0.350
SLC22A11CNOT1psi-mi:“MI:0914”(association)0.350
TMEM17ESYT2psi-mi:“MI:2364”(proximity)0.270
KRASESYT2psi-mi:“MI:2364”(proximity)0.270
CTDSPLESYT2psi-mi:“MI:2364”(proximity)0.270
EPHA2ARHGAP32psi-mi:“MI:2364”(proximity)0.270
FGFR1BLTP3Bpsi-mi:“MI:2364”(proximity)0.270
FGFR4SH3PXD2Bpsi-mi:“MI:2364”(proximity)0.270

BioGRID (90): EFR3B (Affinity Capture-MS), EFR3B (Affinity Capture-MS), EFR3B (Affinity Capture-MS), EFR3B (Proximity Label-MS), EFR3B (Proximity Label-MS), EFR3B (Affinity Capture-MS), EFR3B (Affinity Capture-MS), EFR3B (Affinity Capture-MS), EFR3B (Affinity Capture-MS), EFR3B (Affinity Capture-MS), EFR3B (Affinity Capture-MS), EFR3B (Affinity Capture-MS), EFR3B (Proximity Label-MS), EFR3B (Proximity Label-MS), EFR3B (Synthetic Lethality)

ESM2 similar proteins: A0A571BF63, A0A5F8MPE6, A1A535, A8QHQ0, B0W730, O23463, O46470, O54829, O64851, O82645, P49758, P49802, P49803, P49809, Q058N0, Q0VA04, Q14D04, Q28IH8, Q4R6I5, Q4R7Z7, Q502W7, Q569B9, Q5PQS3, Q5SPP5, Q5XG48, Q5XIR8, Q641A2, Q6ZQ18, Q7T0S7, Q86VD1, Q8BG67, Q8BMD7, Q8CDN8, Q8H1E8, Q8IGJ0, Q8N957, Q8NCR3, Q8NHS4, Q96L03, Q96LI9

Diamond homologs: Q09263, Q14156, Q5SPP5, Q620W3, Q641A2, Q6ZQ18, Q8BG67, Q8IGJ0, Q9Y2G0, Q6C8F7

SIGNOR signaling

1 interactions.

AEffectBMechanism
EFR3B“up-regulates quantity”PI4KAbinding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance72
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
3247406NC_000002.11:g.(?24443763)(25536853_?)delPathogenic

SpliceAI

3959 predictions. Top by Δscore:

VariantEffectΔscore
2:25042315:GTACG:Gdonor_gain1.0000
2:25092997:CTACA:Cacceptor_loss1.0000
2:25092998:TACAG:Tacceptor_loss1.0000
2:25093000:CAGG:Cacceptor_loss1.0000
2:25093001:AG:Aacceptor_gain1.0000
2:25093001:AGGAT:Aacceptor_gain1.0000
2:25093002:G:Aacceptor_loss1.0000
2:25093002:GG:Gacceptor_gain1.0000
2:25093002:GGAT:Gacceptor_gain1.0000
2:25093002:GGATG:Gacceptor_gain1.0000
2:25093126:TATGG:Tdonor_gain1.0000
2:25093127:ATGG:Adonor_gain1.0000
2:25093128:TGG:Tdonor_gain1.0000
2:25093129:GG:Gdonor_gain1.0000
2:25093129:GGG:Gdonor_gain1.0000
2:25093129:GGGTA:Gdonor_loss1.0000
2:25093130:GG:Gdonor_gain1.0000
2:25093131:G:GGdonor_gain1.0000
2:25093131:GT:Gdonor_loss1.0000
2:25093132:T:Adonor_loss1.0000
2:25103636:GGTAC:Gacceptor_gain1.0000
2:25103783:ACTCG:Adonor_gain1.0000
2:25103785:TCG:Tdonor_gain1.0000
2:25103785:TCGG:Tdonor_loss1.0000
2:25103786:CG:Cdonor_gain1.0000
2:25103787:GG:Gdonor_gain1.0000
2:25103788:G:GGdonor_gain1.0000
2:25103789:T:Gdonor_loss1.0000
2:25121667:T:TAacceptor_gain1.0000
2:25121669:ATAGT:Aacceptor_loss1.0000

AlphaMissense

5378 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:25091358:G:TR14M1.000
2:25091360:T:GY15D1.000
2:25091365:A:CK16N1.000
2:25091365:A:TK16N1.000
2:25091370:T:CL18P1.000
2:25091373:T:AV19D1.000
2:25091382:T:AI22N1.000
2:25091384:T:CF23L1.000
2:25091385:T:CF23S1.000
2:25091386:C:AF23L1.000
2:25091386:C:GF23L1.000
2:25093034:T:AL39Q1.000
2:25093034:T:CL39P1.000
2:25093034:T:GL39R1.000
2:25093039:T:AF41I1.000
2:25093039:T:CF41L1.000
2:25093040:T:CF41S1.000
2:25093041:C:AF41L1.000
2:25093041:C:GF41L1.000
2:25093042:T:GY42D1.000
2:25093045:G:CA43P1.000
2:25093046:C:AA43D1.000
2:25093049:T:CL44P1.000
2:25093063:A:GK49E1.000
2:25093065:A:CK49N1.000
2:25093065:A:TK49N1.000
2:25093067:T:AL50H1.000
2:25093067:T:CL50P1.000
2:25093072:C:AR52S1.000
2:25093073:G:CR52P1.000

dbSNP variants (sampled 300 via entrez): RS1000016955 (2:25104124 G>A), RS1000026291 (2:25093080 C>G,T), RS1000029553 (2:25148754 C>A,G,T), RS1000068924 (2:25127404 T>C), RS1000090370 (2:25134283 G>C), RS1000098010 (2:25150500 T>G), RS1000132354 (2:25119407 G>A), RS1000232932 (2:25130034 C>G,T), RS1000264932 (2:25140590 G>A), RS1000272034 (2:25129829 AGCT>A), RS1000288287 (2:25073956 C>T), RS1000302477 (2:25111560 A>G), RS1000305167 (2:25045142 C>A,G,T), RS1000315333 (2:25058295 C>T), RS1000322774 (2:25043210 A>C)

Disease associations

OMIM: gene MIM:616797 | disease phenotypes: MIM:615879, MIM:617190

GenCC curated gene-disease

Mondo (2): Tatton-Brown-Rahman overgrowth syndrome (MONDO:0014382), Shashi-Pena syndrome (MONDO:0014963)

Orphanet (2): Tatton-Brown-Rahman syndrome (Orphanet:404443), Shashi-Pena syndrome (Orphanet:689408)

HPO phenotypes

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

GWAS associations

31 associations (top):

StudyTraitp-value
GCST001255_1Type 1 diabetes4.000000e-09
GCST001935_6Body mass index in non-asthmatics3.000000e-06
GCST004131_107Inflammatory bowel disease3.000000e-07
GCST004132_38Crohn’s disease9.000000e-08
GCST005950_4Body mass index x sex x age interaction (4df test)5.000000e-26
GCST005951_195Body mass index3.000000e-24
GCST005952_4Body mass index (age>50)5.000000e-09
GCST005953_10Body mass index (age <50)6.000000e-20
GCST007293_13Body fat distribution (arm fat ratio)2.000000e-39
GCST007293_41Body fat distribution (arm fat ratio)5.000000e-22
GCST007293_5Body fat distribution (arm fat ratio)2.000000e-21
GCST007294_128Body fat distribution (trunk fat ratio)7.000000e-06
GCST007294_94Body fat distribution (trunk fat ratio)9.000000e-10
GCST008163_518Height1.000000e-13
GCST008163_594Height3.000000e-06
GCST011494_92Daytime nap3.000000e-06
GCST012226_436Waist circumference adjusted for body mass index4.000000e-09
GCST90020024_855A body shape index1.000000e-08
GCST90020024_856A body shape index4.000000e-08
GCST90020024_857A body shape index2.000000e-10
GCST90020025_1589Waist-to-hip ratio adjusted for BMI2.000000e-10
GCST90020025_1590Waist-to-hip ratio adjusted for BMI4.000000e-08
GCST90020027_1598Waist-hip index6.000000e-12
GCST90020027_1599Waist-hip index7.000000e-10
GCST90020028_430Hip circumference adjusted for BMI2.000000e-08
GCST90020028_434Hip circumference adjusted for BMI3.000000e-08
GCST90020029_656Waist circumference adjusted for body mass index5.000000e-09
GCST90020029_782Waist circumference adjusted for body mass index4.000000e-15
GCST90020029_783Waist circumference adjusted for body mass index4.000000e-12
GCST90020029_784Waist circumference adjusted for body mass index6.000000e-18

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0004341body fat distribution
EFO:0007828daytime rest measurement
EFO:0007789BMI-adjusted waist circumference
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008039BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
(+)-JQ1 compoundincreases expression6
Benzo(a)pyreneaffects methylation, decreases expression, increases methylation5
Valproic Acidaffects cotreatment, decreases expression, increases expression4
Estradioldecreases expression, decreases reaction, affects cotreatment, increases expression3
Aflatoxin B1decreases expression, increases methylation3
sodium arseniteincreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Cadmium Chlorideincreases expression2
OTX015increases expression1
FR900359affects phosphorylation1
mivebresibincreases expression1
propionaldehydeincreases expression1
titanium dioxidedecreases expression1
trichostatin Adecreases expression1
sulforaphanedecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
butyraldehydeincreases expression1
perfluorooctanoic acidincreases expression1
benzo(e)pyreneincreases methylation1
potassium chromate(VI)affects cotreatment, decreases expression1
aflatoxin B2affects methylation1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
perfluoro-n-nonanoic acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
perfluorohexanesulfonic acidincreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Decitabineaffects expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03303716Not specifiedRECRUITINGASXL-Related Disorders Natural History Study