EPB41

gene
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Also known as 4.1R

Summary

EPB41 (erythrocyte membrane protein band 4.1, HGNC:3377) is a protein-coding gene on chromosome 1p35.3, encoding Protein 4.1 (P11171). Protein 4.1 is a major structural element of the erythrocyte membrane skeleton.

The protein encoded by this gene, together with spectrin and actin, constitute the red cell membrane cytoskeletal network. This complex plays a critical role in erythrocyte shape and deformability. Mutations in this gene are associated with type 1 elliptocytosis (EL1). Alternatively spliced transcript variants encoding different isoforms have been described for this gene.

Source: NCBI Gene 2035 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): elliptocytosis 1 (Definitive, GenCC) — +1 more curated relationship
  • GWAS associations: 15
  • Clinical variants (ClinVar): 303 total — 17 pathogenic, 17 likely-pathogenic
  • Phenotypes (HPO): 26
  • Druggable target: yes
  • MANE Select transcript: NM_001376013

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:3377
Approved symbolEPB41
Nameerythrocyte membrane protein band 4.1
Location1p35.3
Locus typegene with protein product
StatusApproved
Aliases4.1R
Ensembl geneENSG00000159023
Ensembl biotypeprotein_coding
OMIM130500
Entrez2035

Gene structure

Transcript identifiers

Ensembl transcripts: 88 — 72 protein_coding, 6 retained_intron, 6 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay

ENST00000343067, ENST00000347529, ENST00000349460, ENST00000373797, ENST00000373798, ENST00000373800, ENST00000460378, ENST00000462032, ENST00000482464, ENST00000488277, ENST00000490308, ENST00000636666, ENST00000642643, ENST00000642937, ENST00000643155, ENST00000643173, ENST00000643302, ENST00000643604, ENST00000644342, ENST00000644470, ENST00000644600, ENST00000644780, ENST00000644848, ENST00000645111, ENST00000645184, ENST00000645999, ENST00000646189, ENST00000646260, ENST00000646800, ENST00000646871, ENST00000647103, ENST00000647918, ENST00000648181, ENST00000648891, ENST00000649674, ENST00000649717, ENST00000649992, ENST00000650132, ENST00000650265, ENST00000706361, ENST00000870250, ENST00000870251, ENST00000870252, ENST00000870253, ENST00000870254, ENST00000870255, ENST00000870256, ENST00000921693, ENST00000921694, ENST00000921695, ENST00000921696, ENST00000921697, ENST00000921698, ENST00000921699, ENST00000921700, ENST00000921701, ENST00000921702, ENST00000921703, ENST00000921704, ENST00000921705, ENST00000921706, ENST00000921707, ENST00000921708, ENST00000921709, ENST00000921710, ENST00000921711, ENST00000921712, ENST00000921713, ENST00000921714, ENST00000921715, ENST00000921716, ENST00000921717, ENST00000921718, ENST00000921719, ENST00000921720, ENST00000921721, ENST00000921722, ENST00000921723, ENST00000921724, ENST00000921725, ENST00000921726, ENST00000921727, ENST00000921728, ENST00000921729, ENST00000921730, ENST00000921731, ENST00000921732, ENST00000921733

RefSeq mRNA: 22 — MANE Select: NM_001376013 NM_001166005, NM_001166006, NM_001166007, NM_001376013, NM_001376014, NM_001376015, NM_001376016, NM_001376017, NM_001376018, NM_001376019, NM_001376020, NM_001376021, NM_001376022, NM_001376023, NM_001376024, NM_001376025, NM_001376026, NM_001376027, NM_001376028, NM_004437, NM_203342, NM_203343

CCDS: CCDS330, CCDS331, CCDS53288, CCDS53289, CCDS85947, CCDS90897, CCDS90898, CCDS90899, CCDS90900, CCDS90901, CCDS90902

Canonical transcript exons

ENST00000343067 — 21 exons

ExonStartEnd
ENSE000010650242903582629035923
ENSE000010650252903309329033245
ENSE000010650262899721528997319
ENSE000010650272901822429018442
ENSE000010650292906042229060484
ENSE000010650302901569229015767
ENSE000010650312905310429053312
ENSE000010650322901186529011907
ENSE000010650352903925429039426
ENSE000010650382905881129058852
ENSE000010650392905858929058645
ENSE000010650432903040029030487
ENSE000034617522906498229065158
ENSE000034875552909780729097935
ENSE000034934392911236829112448
ENSE000035075832899333028993542
ENSE000035095312910933629109437
ENSE000035384142911569929115803
ENSE000036866092898743128987905
ENSE000038231032891456928914768
ENSE000038251102911681929120041

Expression profiles

Bgee: expression breadth ubiquitous, 261 present calls, max score 99.17.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 39.5928 / max 2597.6035, expressed in 1716 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
184323.91571622
18457.0381876
18475.1241700
18441.9748356
18460.5189250
18490.4395208
18480.3206167
18520.261278

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
trabecular bone tissueUBERON:000248399.17gold quality
cerebellar hemisphereUBERON:000224597.79gold quality
cerebellar cortexUBERON:000212997.75gold quality
right hemisphere of cerebellumUBERON:001489097.26gold quality
colonic epitheliumUBERON:000039796.36gold quality
cerebellumUBERON:000203796.06gold quality
esophagus squamous epitheliumUBERON:000692094.98gold quality
tonsilUBERON:000237294.78gold quality
bloodUBERON:000017894.77gold quality
amniotic fluidUBERON:000017394.06gold quality
epithelium of nasopharynxUBERON:000195193.82gold quality
monocyteCL:000057693.17gold quality
bone marrowUBERON:000237193.06gold quality
granulocyteCL:000009493.01gold quality
mucosa of sigmoid colonUBERON:000499392.64gold quality
leukocyteCL:000073892.51gold quality
lymph nodeUBERON:000002992.49gold quality
colonic mucosaUBERON:000031792.48gold quality
gingival epitheliumUBERON:000194992.39gold quality
upper leg skinUBERON:000426292.27gold quality
mononuclear cellCL:000084292.18gold quality
cardia of stomachUBERON:000116291.72gold quality
pylorusUBERON:000116691.66gold quality
gingivaUBERON:000182891.46gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451191.26gold quality
jejunal mucosaUBERON:000039991.17gold quality
ganglionic eminenceUBERON:000402390.49gold quality
buccal mucosa cellCL:000233690.48gold quality
ventricular zoneUBERON:000305390.44gold quality
cerebellar vermisUBERON:000472090.40gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 6.

ExperimentMarker?Max mean expression
E-MTAB-11121yes1213.15
E-MTAB-9221yes11.68
E-HCAD-5yes9.58
E-MTAB-6678yes4.41
E-CURD-112yes3.82
E-MTAB-10042no401.36
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): HOXA7, ZNF148

miRNA regulators (miRDB)

129 targeting EPB41, 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-3613-3P100.0076.367965
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-3646100.0073.565283
HSA-MIR-4481100.0066.421669
HSA-MIR-6748-5P100.0065.811057
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-8485100.0077.574731
HSA-MIR-4425100.0067.591049
HSA-MIR-4262100.0073.263931
HSA-MIR-4692100.0067.322066
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-477599.9875.006394
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-4745-5P99.9865.951028
HSA-MIR-6793-5P99.9765.95758
HSA-MIR-590-3P99.9674.346478
HSA-MIR-381-3P99.9371.872854
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-449399.9066.48977

Literature-anchored findings (GeneRIF, showing 40)

  • Reassignment of the EPB4.1 gene to 1p36 and assessment of its involvement in neuroblastomas. (PMID:11737230)
  • With deletions or mutations, the ability of the 8 amino acid motif (LKKNFMES) of the spectrin-actin-binding domain of erythrocyte protein 4.1 recombinant peptides to form ternary complexes with spectrin and actin is remarkably diminished. (PMID:12044158)
  • falcipain-2-mediated cleavage of protein 4.1 occurs immediately after lysine 437, which lies within a region of the spectrin-actin-binding domain critical for erythrocyte membrane stability. (PMID:12130521)
  • A splicing alteration of pre-mRNA generates 2 protein isoforms with distinct assembly to spindle poles in mitotic cells (PMID:12239178)
  • A 4.1R isoform expressing the leucine-rich sequence binds to the export receptor CRM1 in a RanGTP-dependent fashion, whereas this does not occur in a mutant whose two conserved hydrophobic residues are substituted (PMID:12427749)
  • synthesis of structurally distinct 4.1R protein isoforms in various cell types is regulated by a novel mechanism requiring coordination between upstream transcription initiation events and downstream alternative splicing events (PMID:12522012)
  • A novel member of the protein 4.1 family was cloned; it has focal expression in the ovary. (PMID:12601556)
  • protein 4.1R has a role in recruiting hDlg to the lateral membrane in epithelial cells (PMID:12807908)
  • Protein 4.1R functions as an important tumor suppressor in the molecular pathogenesis of meningioma (PMID:12901833)
  • interaction with nuclear actin during nuclear assembly in vitro (PMID:12960380)
  • alpha-spectrin ubiquitination at repeats 20 and 21 increases the dissociation of the spectrin-protein-4.1-actin ternary complex thereby regulating protein 4.1’s ability to stimulate the spectrin-actin interaction (PMID:15040429)
  • 135-kDa non-erythroid 4.1R has a role in cell division (PMID:15184364)
  • protein 4.1R mitotic regulation involves phosphorylation by cdc2 kinase (PMID:15525677)
  • 4.1R plays a key role at the centrosome, contributing to the maintenance of a radial microtubule organization (PMID:15564380)
  • protein 4.1 phosphorylation modulates erythrocyte membrane mechanical function (PMID:15611095)
  • Alternative splicing isoforms are present in muscular dystsrophy skeletal muscle. (PMID:15714879)
  • 4.1R loss of expression was statistically more common in ependymomas. (PMID:15731777)
  • We speculate that over the repetitive cycles of heart muscle contraction and relaxation, 4.1s are likely to locate, support, and coordinate functioning of key membrane-bound macromolecular assemblies. (PMID:15834631)
  • 4.1R binds to the separate calponin homology CH1 and CH2 domains of beta I spectrin. (PMID:16060676)
  • EPB41 gene expression was unchanged in all analyzed meningiomas. This suggests that involvement of the EPB41 gene (4.1R protein) in meningioma pathogenesis should be reconsidered. (PMID:16157202)
  • interaction of protein 4.1 with TRPC4 is required for activation of the endothelial ISOC channel. (PMID:16254212)
  • protein 4.1R interactions with membrane proteins are regulated by Ca2+ and calmodulin [review] (PMID:16368534)
  • Fox-1 and Fox-2 splicing factors have roles in alternative splicing of protein 4.1R (PMID:16537540)
  • 4.1R60 isoforms are constitutively self-associated, whereas 4.1R80 and 4.1R135 self-association is prevented by intramolecular interactions. (PMID:16881872)
  • The interaction of Plasmodium falciparum EBA-181 with the highly conserved 10 kDa domain of 4.1R provides new insight into the molecular mechanisms utilized by P. falciparum during erythrocyte entry (PMID:17087826)
  • A decreased expression pattern of the 4.1R protein was observed in the erythrocytes from patients with atypical NA. (PMID:17298666)
  • A regulated splicing event in protein 4.1R pre-mRNA-the inclusion of exon 16-encoding peptides for spectrin-actin binding-occurs in late erythroid differentiation (PMID:17715393)
  • A deficit in protein 4.1R is recurrent in myeloid malignancies and should be particularly investigated when deletion del (20 q) is present, since this chromosomal abnormality was present in four out of six patients. (PMID:17994571)
  • In the 4.1R gene, intrasplicing ultimately determines N-terminal protein structure and function. (PMID:18079699)
  • 4.1R makes crucial contributions to the structural integrity of centrosomes & mitotic spindles which normally enable mitosis and anaphase to proceed with coordinated precision. (PMID:18212055)
  • Findings enable us to offer potential new insights into the differential contribution of 4.1R isoforms, 4.1R(80) and 4.1R(135), to membrane assembly during terminal erythroid differentiation. (PMID:18691159)
  • p55 binds to two distinct sites within the FERM domain, and the alternatively spliced exon 5 is necessary for the membrane targeting of protein 4.1R in epithelial cells. (PMID:18952129)
  • Study reports the first NMR-derived structure of the 4.1R FERM alpha-lobe domain and propose a new glycophorin C-binding site on the 4.1R FERM alpha-lobe domain, based on our NMR experiments. (PMID:19338061)
  • Proteins in the membrane skeleton protein 4.1 family are weakly expressed in non-small cell lung cancer and are related to tumor cell differentiation. (PMID:19624891)
  • 4.1R gene expression involves transcriptional regulation coupled with a complex splicing regulatory network. (PMID:19729518)
  • 4.1R plays a role in the phosphatidylserine exposure signaling pathway that is of fundamental importance in red cell turnover. (PMID:19794081)
  • Data suggest that one or both of proteins 4.1 and 4.2 cause a portion of band 3 to localize near the spectrin-actin junctions and provide another point of attachment between the membrane skeleton and the lipid bilayer. (PMID:20007969)
  • Four EPB41 SNPs showed allelic and genotypic associations with MP in first stage. In the second stage, the allele rs4654388 showed the strongest significant association with MP. rs4654388 G-allele was associated with a significantly increased risk of MP. (PMID:20797695)
  • in addition to two known minor shortened and stable spliceoforms, a 4.1R splicing mutation activates an intronic cryptic splice site, which results in a nonsense mRNA major isoform, targeted to degradation in intact cells by Nonsense-mediated mRNA decay. (PMID:20863723)
  • Data provide evidence that 4.1R has functional interactions with emerin and A-type lamin that impact upon nuclear architecture, centrosome-nuclear envelope association and the regulation of beta-catenin transcriptional co-activator activity. (PMID:21486941)

Cross-species orthologs

10 orthologs

OrganismSymbolGene ID
danio_rerioepb41aENSDARG00000099283
mus_musculusEpb41ENSMUSG00000028906
rattus_norvegicusEpb41ENSRNOG00000010037
drosophila_melanogasteryrtFBGN0004049
drosophila_melanogastercoraFBGN0010434
drosophila_melanogasterFrmd5FBGN0032225
caenorhabditis_eleganserm-1WBGENE00001333
caenorhabditis_elegansfrm-1WBGENE00001488
caenorhabditis_elegansWBGENE00001489
caenorhabditis_elegansfrm-4WBGENE00001491

Paralogs (10): MYLIP (ENSG00000007944), EPB41L2 (ENSG00000079819), EPB41L3 (ENSG00000082397), EPB41L1 (ENSG00000088367), EPB41L4B (ENSG00000095203), EPB41L5 (ENSG00000115109), EPB41L4A (ENSG00000129595), FRMD6 (ENSG00000139926), FRMD5 (ENSG00000171877), FRMD3 (ENSG00000172159)

Protein

Protein identifiers

Protein 4.1P11171 (reviewed: P11171)

Alternative names: 4.1R, Band 4.1, EPB4.1, Erythrocyte membrane protein band 4.1

All UniProt accessions (24): P11171, A0A1B0GWG0, A0A2R8Y420, A0A2R8Y4N6, A0A2R8Y570, A0A2R8Y5C8, A0A2R8Y5G2, A0A2R8Y5Z6, A0A2R8Y6D0, A0A2R8Y6G5, A0A2R8Y6T6, A0A2R8Y783, A0A2R8Y7N0, A0A2R8Y7Y3, A0A2R8YCW8, A0A2R8YD30, A0A2R8YFR9, A0A2R8YFU8, A0A2U3TZH6, A0A3B3ITC5, A0A3B3ITP0, A0A3B3IU06, A0A3B3IUD6, A0A994J847

UniProt curated annotations — full annotation on UniProt →

Function. Protein 4.1 is a major structural element of the erythrocyte membrane skeleton. It plays a key role in regulating membrane physical properties of mechanical stability and deformability by stabilizing spectrin-actin interaction. Recruits DLG1 to membranes. Required for dynein-dynactin complex and NUMA1 recruitment at the mitotic cell cortex during anaphase.

Subunit / interactions. Binds with a high affinity to glycophorin and with lower affinity to band III protein. Associates with the nuclear mitotic apparatus. Interacts with calmodulin. Interacts with CPAP. Interacts with DLG1. Also found to associate with contractile apparatus and tight junctions. Interacts with NUMA1; this interaction is negatively regulated by CDK1 during metaphase and promotes anaphase-specific localization of NUMA1 in symmetrically dividing cells. Interacts with ATP2B1; regulates small intestinal calcium absorption through regulation of membrane expression of ATP2B1.

Subcellular location. Cytoplasm. Cytoskeleton. Cell cortex. Nucleus.

Post-translational modifications. Phosphorylated at multiple sites by different protein kinases and each phosphorylation event selectively modulates the protein’s functions. Phosphorylation on Tyr-660 reduces the ability of 4.1 to promote the assembly of the spectrin/actin/4.1 ternary complex. O-glycosylated; contains N-acetylglucosamine side chains in the C-terminal domain.

Disease relevance. Elliptocytosis 1 (EL1) [MIM:611804] A Rhesus-linked form of hereditary elliptocytosis, a genetically heterogeneous, autosomal dominant hematologic disorder. It is characterized by variable hemolytic anemia and elliptical or oval red cell shape. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (7)

UniProt IDNamesCanonical?
P11171-11yes
P11171-22
P11171-33
P11171-44, Erythroid
P11171-55, Non-erythroid A
P11171-66, Non-erythroid B
P11171-77

RefSeq proteins (22): NP_001159477, NP_001159478, NP_001159479, NP_001362942, NP_001362943, NP_001362944, NP_001362945, NP_001362946, NP_001362947, NP_001362948, NP_001362949, NP_001362950, NP_001362951, NP_001362952, NP_001362953, NP_001362954, NP_001362955, NP_001362956, NP_001362957, NP_004428, NP_976217, NP_976218 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000299FERM_domainDomain
IPR000798Ez/rad/moesin-likeFamily
IPR007477SAB_domDomain
IPR008379Band_4.1_CDomain
IPR011993PH-like_dom_sfHomologous_superfamily
IPR014352FERM/acyl-CoA-bd_prot_sfHomologous_superfamily
IPR014847FADomain
IPR018979FERM_NDomain
IPR018980FERM_PH-like_CDomain
IPR019747FERM_CSConserved_site
IPR019748FERM_centralDomain
IPR019749Band_41_domainDomain
IPR021187EPB4.1_FERM_F1Domain
IPR029071Ubiquitin-like_domsfHomologous_superfamily
IPR035963FERM_2Homologous_superfamily

Pfam: PF00373, PF04382, PF05902, PF08736, PF09379, PF09380

UniProt features (94 total): modified residue 26, strand 14, helix 12, sequence conflict 10, compositionally biased region 9, region of interest 8, splice variant 8, mutagenesis site 2, turn 2, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
3QIJX-RAY DIFFRACTION1.8
1GG3X-RAY DIFFRACTION2.8
2RQ1SOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P11171-F163.720.31

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 (26): 14, 60, 84, 85, 95, 104, 121, 149, 151, 152, 188, 191, 222, 378, 521, 540, 542, 555, 660, 664 …

Mutagenesis-validated functional residues (2):

PositionPhenotype
60loss of cdk1-mediated phosphorylation. abolishes targeting onto the mitotic spindle; when associated with a-712.
712loss of cdk1-mediated phosphorylation. abolishes targeting onto the mitotic spindle; when associated with a-60.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6794361Neurexins and neuroligins

MSigDB gene sets: 361 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, ATF_B, GOBP_DIGESTION, BROWNE_HCMV_INFECTION_6HR_DN, GOBP_RESPONSE_TO_FLUID_SHEAR_STRESS, PEREZ_TP63_TARGETS, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION, AREB6_01, KEGG_TIGHT_JUNCTION, RIZKI_TUMOR_INVASIVENESS_3D_DN, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_MONOATOMIC_CATION_TRANSPORT, AGGCACT_MIR5153P, PUJANA_CHEK2_PCC_NETWORK, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY

GO Biological Process (7): actin cytoskeleton organization (GO:0030036), cortical actin cytoskeleton organization (GO:0030866), actomyosin structure organization (GO:0031032), cell division (GO:0051301), regulation of calcium ion transport (GO:0051924), regulation of intestinal absorption (GO:1904478), positive regulation of protein localization to cell cortex (GO:1904778)

GO Molecular Function (9): actin binding (GO:0003779), structural constituent of cytoskeleton (GO:0005200), calmodulin binding (GO:0005516), 1-phosphatidylinositol binding (GO:0005545), spectrin binding (GO:0030507), phosphoprotein binding (GO:0051219), structural molecule activity (GO:0005198), protein binding (GO:0005515), cytoskeletal protein binding (GO:0008092)

GO Cellular Component (15): cytosol (GO:0005829), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), cell cortex (GO:0005938), spectrin-associated cytoskeleton (GO:0014731), basolateral plasma membrane (GO:0016323), nuclear body (GO:0016604), cell junction (GO:0030054), cortical cytoskeleton (GO:0030863), protein-containing complex (GO:0032991), intercellular bridge (GO:0045171), mitotic spindle (GO:0072686), nucleus (GO:0005634), cytoplasm (GO:0005737), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Protein-protein interactions at synapses1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
cytoskeleton3
protein binding3
cytoskeleton organization2
actin cytoskeleton organization2
cytoskeletal protein binding2
cytoplasm2
intracellular membraneless organelle2
cell periphery2
actin filament-based process1
cortical cytoskeleton organization1
cellular process1
calcium ion transport1
regulation of metal ion transport1
regulation of digestive system process1
intestinal absorption1
protein localization to cell cortex1
positive regulation of protein localization to cell periphery1
regulation of protein localization to cell cortex1
structural molecule activity1
phospholipid binding1
protein-containing complex binding1
molecular_function1
binding1
membrane1
basal plasma membrane1
plasma membrane region1
nucleoplasm1
cell cortex1
cellular_component1
spindle1
intracellular membrane-bounded organelle1
intracellular anatomical structure1

Protein interactions and networks

STRING

1576 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EPB41ANK1P16157997
EPB41GYPCP04921996
EPB41ANK3Q12955996
EPB41ANK2Q01484996
EPB41ADD1P35611994
EPB41ADD2P35612993
EPB41ADD3Q9UEY8993
EPB41DMTNQ08495989
EPB41SPTBP11277972
EPB41EZRP15311935
EPB41CADM1Q9BY67917
EPB41RDXP35241894
EPB41DLG1Q12959892
EPB41SLC4A1P02730890
EPB41MPP1Q00013871

IntAct

182 interactions, top by confidence:

ABTypeScore
MED4MED19psi-mi:“MI:2364”(proximity)0.900
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
YWHAGBLTP3Bpsi-mi:“MI:0914”(association)0.640
DDAH2EPB41L2psi-mi:“MI:0914”(association)0.640
SNRPBSART1psi-mi:“MI:0914”(association)0.640
YWHAHBLTP3Bpsi-mi:“MI:0914”(association)0.570
EPB41L1AP3B1psi-mi:“MI:0914”(association)0.530
EPB41L3AP3B1psi-mi:“MI:0914”(association)0.530
YWHAQPLEKHG3psi-mi:“MI:0914”(association)0.480
MYL12Bpsi-mi:“MI:0914”(association)0.460
CASKEPB41psi-mi:“MI:0407”(direct interaction)0.440
NSD3EPB41psi-mi:“MI:0915”(physical association)0.400
EPB41GYPCpsi-mi:“MI:0915”(physical association)0.400
ORF73ECI2psi-mi:“MI:0914”(association)0.350
BCAR1PSMD11psi-mi:“MI:0914”(association)0.350
BCAR1MYO1Cpsi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
LRRK2psi-mi:“MI:0914”(association)0.350
YWHAGC1orf226psi-mi:“MI:0914”(association)0.350
KDM4CSMCHD1psi-mi:“MI:0914”(association)0.350
EEF2KCNOT1psi-mi:“MI:0914”(association)0.350
CHEK2EPB41psi-mi:“MI:0914”(association)0.350
NFE2L2MYO1Dpsi-mi:“MI:0914”(association)0.350
FGFR3U2SURPpsi-mi:“MI:0914”(association)0.350
MAPTSHTN1psi-mi:“MI:0914”(association)0.350

BioGRID (170): EPB41 (Two-hybrid), RWDD2B (Two-hybrid), ZCCHC10 (Two-hybrid), EPB41 (Affinity Capture-MS), EPB41 (Co-fractionation), SF3A3 (Co-fractionation), EPB41 (Affinity Capture-MS), EPB41 (Proximity Label-MS), EPB41 (Proximity Label-MS), EPB41 (Proximity Label-MS), EPB41 (Affinity Capture-RNA), EPB41 (Affinity Capture-MS), EPB41 (Affinity Capture-RNA), MYH9 (Affinity Capture-MS), EPB41 (Affinity Capture-MS)

ESM2 similar proteins: A2AD83, A4Q9F0, A6QP06, A7KAX9, B2RYE5, B4K6T8, F7E540, G5EEW9, O00443, O13839, O43283, O96838, P11171, P11434, P48193, Q12923, Q14693, Q22744, Q3V0G7, Q5FVG2, Q5R8N8, Q5R8X7, Q5RAY1, Q61194, Q64512, Q6DTM3, Q6GPD0, Q6Q7P4, Q6ZT98, Q6ZUT3, Q811P8, Q8BGS1, Q8BPQ7, Q8CHB8, Q8K3Y6, Q8WYB5, Q91573, Q91ZP3, Q96HH9, Q99PI5

Diamond homologs: A2A2Y4, A2AD83, A2ALK8, B2RYE5, F1LYQ8, F1P065, F8VPU2, O43491, O57457, O70318, O94887, P11171, P11434, P26045, P28191, P29074, P48193, P52963, Q0P4Q4, Q54K81, Q58CU2, Q5FVG2, Q5R803, Q5RAB8, Q6P5H6, Q6Q7P4, Q6ZUT3, Q7Z6J6, Q8BGS1, Q8BHD4, Q91VS8, Q9H329, Q9H4G0, Q9HCM4, Q9HCS5, Q9JMC8, Q9MYU8, Q9N179, Q9V8R9, Q9WTP0

SIGNOR signaling

4 interactions.

AEffectBMechanism
EGFRdown-regulatesEPB41phosphorylation
EPB41“up-regulates activity”NUMA1relocalization
EPB41“form complex”“4.1 complex”binding
EPB41“up-regulates activity”DLG1relocalization

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 194 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
Antigen processing: Ub, ATP-independent proteasomal degradation724.4×3e-07
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex520.5×4e-05
Vif-mediated degradation of APOBEC3G1015.5×2e-07
RHO GTPases activate PKNs815.5×8e-07
Regulation of activated PAK-2p34 by proteasome mediated degradation915.3×3e-07
AUF1 (hnRNP D0) binds and destabilizes mRNA1015.1×2e-07
GSK3B and BTRC:CUL1-mediated-degradation of NFE2L21015.1×2e-07
Regulation of ornithine decarboxylase (ODC)914.9×3e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic17
Likely pathogenic17
Uncertain significance164
Likely benign40
Benign18

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
16711NM_203342.2(EPB41):c.-159_159delPathogenic
16712NM_004437.3(EPB41):c.1219_1587delPathogenic
16713NM_004437.3(EPB41):c.1219_1458delPathogenic
16714NM_001376013.1(EPB41):c.629T>G (p.Met210Arg)Pathogenic
16715NM_001376013.1(EPB41):c.629T>C (p.Met210Thr)Pathogenic
221297NM_001376013.1(EPB41):c.1071_1077del (p.Asn358fs)Pathogenic
2779958NM_001376013.1(EPB41):c.2143C>T (p.Arg715Ter)Pathogenic
2819907NM_001376013.1(EPB41):c.1473dup (p.Thr492fs)Pathogenic
3341889NM_001376013.1(EPB41):c.1059dup (p.Lys354Ter)Pathogenic
3667832NM_001376013.1(EPB41):c.820C>T (p.Gln274Ter)Pathogenic
3727875NM_001376013.1(EPB41):c.1301G>A (p.Trp434Ter)Pathogenic
3766780NM_001376013.1(EPB41):c.741del (p.Glu248fs)Pathogenic
4279438GRCh37/hg19 1p35.3(chr1:29242759-29427780)x1Pathogenic
4728387NM_001376013.1(EPB41):c.659_660del (p.Thr220fs)Pathogenic
4736259NM_001376013.1(EPB41):c.2179G>T (p.Glu727Ter)Pathogenic
4779011NM_001376013.1(EPB41):c.742G>T (p.Glu248Ter)Pathogenic
620455NM_001376013.1(EPB41):c.666T>G (p.Tyr222Ter)Pathogenic
1163136NM_001376013.1(EPB41):c.1744dup (p.Thr582fs)Likely pathogenic
1324333NM_001376013.1(EPB41):c.712C>T (p.Arg238Ter)Likely pathogenic
1324334NM_001376013.1(EPB41):c.1175del (p.Lys392fs)Likely pathogenic
1330707NM_001376013.1(EPB41):c.2065A>T (p.Lys689Ter)Likely pathogenic
2440049NM_001376013.1(EPB41):c.1330dup (p.Arg444fs)Likely pathogenic
2446433NM_001376013.1(EPB41):c.768G>A (p.Trp256Ter)Likely pathogenic
2631490NM_001376013.1(EPB41):c.1652C>A (p.Ser551Ter)Likely pathogenic
2690597NM_001376013.1(EPB41):c.2085_2089del (p.Val696fs)Likely pathogenic
2855191NM_001376013.1(EPB41):c.1636+1G>TLikely pathogenic
3391109NM_001376013.1(EPB41):c.902C>G (p.Thr301Arg)Likely pathogenic
4081367NM_001376013.1(EPB41):c.818del (p.Lys273fs)Likely pathogenic
4081369NM_001376013.1(EPB41):c.1295del (p.Phe432fs)Likely pathogenic
4081370NM_001376013.1(EPB41):c.1609A>T (p.Lys537Ter)Likely pathogenic

SpliceAI

4279 predictions. Top by Δscore:

VariantEffectΔscore
1:28887208:CAGG:Cdonor_loss1.0000
1:28887211:G:GAdonor_loss1.0000
1:28987426:A:AGacceptor_gain1.0000
1:28987427:A:Gacceptor_gain1.0000
1:28987428:T:Gacceptor_gain1.0000
1:28987429:A:AGacceptor_gain1.0000
1:28987430:G:GGacceptor_gain1.0000
1:28987430:GC:Gacceptor_gain1.0000
1:28987430:GCA:Gacceptor_gain1.0000
1:28987430:GCAA:Gacceptor_gain1.0000
1:28987430:GCAAC:Gacceptor_gain1.0000
1:28987906:G:GCdonor_loss1.0000
1:28987907:T:Adonor_loss1.0000
1:28993303:T:Aacceptor_gain1.0000
1:29015686:TTATA:Tacceptor_loss1.0000
1:29015687:TATAG:Tacceptor_loss1.0000
1:29015689:TAG:Tacceptor_loss1.0000
1:29015691:GGT:Gacceptor_gain1.0000
1:29015763:ACAAG:Adonor_loss1.0000
1:29015764:CAAGG:Cdonor_loss1.0000
1:29015768:G:GAdonor_loss1.0000
1:29015769:T:Adonor_loss1.0000
1:29018439:ACAG:Adonor_loss1.0000
1:29018442:GG:Gdonor_loss1.0000
1:29018443:G:Adonor_loss1.0000
1:29030388:A:AGacceptor_gain1.0000
1:29030389:T:Gacceptor_gain1.0000
1:29030393:A:AGacceptor_gain1.0000
1:29030394:T:Gacceptor_gain1.0000
1:29030396:A:AGacceptor_gain1.0000

AlphaMissense

5681 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:29018244:T:CL309P1.000
1:29030419:G:CA382P1.000
1:29033118:T:CL413P1.000
1:29033120:G:CG414R1.000
1:29033139:T:CL420P1.000
1:29033145:T:AV422D1.000
1:29033174:T:CF432L1.000
1:29033175:T:CF432S1.000
1:29033176:C:AF432L1.000
1:29033176:C:GF432L1.000
1:29033180:T:AW434R1.000
1:29033180:T:CW434R1.000
1:29033182:G:CW434C1.000
1:29033182:G:TW434C1.000
1:29033193:T:CL438P1.000
1:29033195:A:GK439E1.000
1:29033208:A:TK443I1.000
1:29033220:T:CF447S1.000
1:29033226:T:AI449N1.000
1:29033228:A:GK450E1.000
1:29035853:T:CF465L1.000
1:29035854:T:CF465S1.000
1:29035855:C:AF465L1.000
1:29035855:C:GF465L1.000
1:29035860:T:CL467P1.000
1:29035878:C:AA473D1.000
1:29035889:T:AW477R1.000
1:29035889:T:CW477R1.000
1:29035891:G:CW477C1.000
1:29035891:G:TW477C1.000

dbSNP variants (sampled 300 via entrez): RS1000014912 (1:29119298 ATG>A), RS1000015671 (1:28924821 G>C), RS1000022462 (1:29037490 C>T), RS1000037036 (1:29057765 A>G,T), RS1000055003 (1:29106735 G>A,T), RS1000060399 (1:29106449 T>C), RS1000065497 (1:29011228 G>T), RS1000068067 (1:28925169 T>C), RS1000071955 (1:29025713 T>C), RS1000085601 (1:29057486 T>G), RS1000086789 (1:28965428 A>G,T), RS1000090746 (1:29106460 T>C), RS1000120286 (1:29113276 G>A), RS1000121131 (1:29042492 T>G), RS1000130058 (1:28971180 CTTTTTTTTTTTTTTTTTT>C,CTTTT,CTTTTT,CTTTTTT,CTTTTTTT,CTTTTTTTT,CTTTTTTTTT,CTTTTTTTTTT,CTTTTTTTTTTT,CTTTTTTTTTTTT,CTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT)

Disease associations

OMIM: gene MIM:130500 | disease phenotypes: MIM:611804

GenCC curated gene-disease

DiseaseClassificationInheritance
elliptocytosis 1DefinitiveSemidominant
hereditary elliptocytosisSupportiveAutosomal dominant

Mondo (2): elliptocytosis 1 (MONDO:0012731), hereditary elliptocytosis (MONDO:0017319)

Orphanet (1): Hereditary elliptocytosis (Orphanet:288)

HPO phenotypes

26 total (26 of 26 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000952Jaundice
HP:0000980Pallor
HP:0001081Cholelithiasis
HP:0001744Splenomegaly
HP:0001789Hydrops fetalis
HP:0001877Abnormal erythrocyte morphology
HP:0001878Hemolytic anemia
HP:0001923Reticulocytosis
HP:0001945Fever
HP:0002007Frontal bossing
HP:0002027Abdominal pain
HP:0002904Hyperbilirubinemia
HP:0003265Neonatal hyperbilirubinemia
HP:0003546Exercise intolerance
HP:0004445Elliptocytosis
HP:0004446Stomatocytosis
HP:0004447Poikilocytosis
HP:0004804Congenital hemolytic anemia
HP:0005502Increased red cell osmotic fragility
HP:0006579Prolonged neonatal jaundice
HP:0008897Postnatal growth retardation
HP:0012378Fatigue
HP:0025143Chills
HP:0200042Skin ulcer

GWAS associations

15 associations (top):

StudyTraitp-value
GCST002337_76Amyotrophic lateral sclerosis (sporadic)6.000000e-06
GCST007277_1Tourette syndrome2.000000e-06
GCST010083_183Hemoglobin levels1.000000e-09
GCST012325_1HDL levels x SSRI defined daily dose interaction in schizophrenia or bipolar disorder4.000000e-07
GCST90002385_607High light scatter reticulocyte count2.000000e-11
GCST90002386_312High light scatter reticulocyte percentage of red cells7.000000e-11
GCST90002391_58Mean corpuscular hemoglobin concentration1.000000e-11
GCST90002396_122Mean reticulocyte volume5.000000e-12
GCST90002396_123Mean reticulocyte volume1.000000e-13
GCST90002396_124Mean reticulocyte volume7.000000e-74
GCST90002397_622Mean spheric corpuscular volume4.000000e-10
GCST90002397_623Mean spheric corpuscular volume4.000000e-77
GCST90002401_11Platelet distribution width6.000000e-16
GCST90002405_600Reticulocyte count9.000000e-24
GCST90002406_137Reticulocyte fraction of red cells6.000000e-25

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0004509hemoglobin measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0005658response to selective serotonin reuptake inhibitor
EFO:0007986reticulocyte count
EFO:0004528mean corpuscular hemoglobin concentration
EFO:0010701mean reticulocyte volume
EFO:0007984platelet component distribution width

MeSH disease descriptors (2)

DescriptorNameTree numbers
D004612Elliptocytosis, HereditaryC15.378.050.141.150.365; C16.320.070.365
C567520Elliptocytosis 1 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066965 (SINGLE PROTEIN)

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

PharmGKB clinical annotations

1 annotations.

VariantTypeLevelDrugsPhenotypes
rs6702335Efficacy3bupropion;nicotineTobacco Use Disorder

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs6702335EPB4133.251bupropion;nicotine

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.11Kd7.837nMCHEMBL5653589
8.11ED507.837nMCHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148322: Binding affinity to human EPB41 incubated for 45 mins by Kinobead based pull down assaykd0.0078uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, increases methylation5
sodium arseniteaffects methylation, decreases expression, increases abundance, increases expression4
bisphenol Adecreases expression, increases expression, increases methylation3
Acetaminophendecreases expression3
Air Pollutantsdecreases expression, increases abundance, increases expression2
Arsenicaffects methylation, increases abundance, increases expression2
Benzo(a)pyreneaffects methylation, decreases expression2
Cyclosporineincreases expression2
aristolochic acid Idecreases expression1
GSK-J4increases expression1
FR900359affects phosphorylation1
9-hydroxyoctadecadienoic acidincreases expression1
pirinixic acidincreases expression, affects binding, increases activity1
trichostatin Aincreases expression1
11-nor-delta(9)-tetrahydrocannabinol-9-carboxylic acidaffects methylation, increases abundance1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
butyraldehydedecreases expression1
manganese chlorideincreases abundance, increases expression1
potassium chromate(VI)increases expression1
coumarindecreases phosphorylation1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent iondecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
bisphenol Sdecreases methylation1
LDN 193189affects cotreatment, increases expression1
Decitabineaffects expression1
Sunitinibincreases expression1
Vorinostatdecreases expression1
Caffeinedecreases phosphorylation1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651364BindingBinding affinity to human EPB41 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00723567Not specifiedCOMPLETEDA Novel Mutation of the Spectrin Gene
NCT01923376Not specifiedWITHDRAWNHepatic Encephalopathy: Lactulose or Polyethylene Glycol (H.E.L.P.)