EGFLAM

gene
On this page

Also known as FLJ39155AGRINLAGRNLPIKA

Summary

EGFLAM (EGF like, fibronectin type III and laminin G domains, HGNC:26810) is a protein-coding gene on chromosome 5p13.2-p13.1, encoding Pikachurin (Q63HQ2). Involved in both the retinal photoreceptor ribbon synapse formation and physiological functions of visual perception.

Predicted to enable calcium ion binding activity and glycosaminoglycan binding activity. Predicted to act upstream of or within extracellular matrix organization and positive regulation of cell-substrate adhesion. Part of cell surface.

Source: NCBI Gene 133584 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 199 total
  • MANE Select transcript: NM_152403

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26810
Approved symbolEGFLAM
NameEGF like, fibronectin type III and laminin G domains
Location5p13.2-p13.1
Locus typegene with protein product
StatusApproved
AliasesFLJ39155, AGRINL, AGRNL, PIKA
Ensembl geneENSG00000164318
Ensembl biotypeprotein_coding
OMIM617683
Entrez133584

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 8 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000322350, ENST00000336740, ENST00000354891, ENST00000397202, ENST00000397210, ENST00000504709, ENST00000506135, ENST00000508131, ENST00000508868, ENST00000513131, ENST00000514476

RefSeq mRNA: 4 — MANE Select: NM_152403 NM_001205301, NM_152403, NM_182798, NM_182801

CCDS: CCDS3924, CCDS3925, CCDS47199, CCDS56363

Canonical transcript exons

ENST00000322350 — 22 exons

ExonStartEnd
ENSE000012432463846290838463011
ENSE000012434063843827538438455
ENSE000012434143843513738435253
ENSE000012434233843117738431288
ENSE000012435013845831138458394
ENSE000013451053846383238465480
ENSE000016215853840612638406241
ENSE000016688263840682838407146
ENSE000017310423840900438409104
ENSE000017361633840780538407905
ENSE000017548623837029638370462
ENSE000017560783841806638418255
ENSE000034747283833752038337629
ENSE000034759563835219638352331
ENSE000034986253842496738425092
ENSE000035244693833869838338781
ENSE000035304373841250438412648
ENSE000035590753835050138350618
ENSE000035944673844830138448379
ENSE000036220133842700938427252
ENSE000036669333845131538451458
ENSE000038479473825855938258851

Expression profiles

Bgee: expression breadth ubiquitous, 179 present calls, max score 94.09.

FANTOM5 (CAGE): breadth broad, TPM avg 3.1662 / max 96.3490, expressed in 693 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
561901.4146471
561870.8983230
561890.6195290
561860.184488
2035290.026311
561880.01243
2035300.01084

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
gastrocnemiusUBERON:000138894.09gold quality
hindlimb stylopod muscleUBERON:000425294.07gold quality
muscle of legUBERON:000138393.68gold quality
tibialis anteriorUBERON:000138593.49gold quality
deltoidUBERON:000147691.21gold quality
vastus lateralisUBERON:000137990.80gold quality
omental fat padUBERON:001041490.79gold quality
quadriceps femorisUBERON:000137790.71gold quality
tibial nerveUBERON:000132390.69gold quality
peritoneumUBERON:000235890.65gold quality
adipose tissue of abdominal regionUBERON:000780890.32gold quality
apex of heartUBERON:000209890.30gold quality
skeletal muscle tissueUBERON:000113490.13gold quality
biceps brachiiUBERON:000150789.72gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450289.01gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.98gold quality
right ovaryUBERON:000211888.66gold quality
left ovaryUBERON:000211988.38gold quality
subcutaneous adipose tissueUBERON:000219088.20gold quality
popliteal arteryUBERON:000225088.05gold quality
tibial arteryUBERON:000761088.05gold quality
adipose tissueUBERON:000101386.99gold quality
muscle tissueUBERON:000238586.79gold quality
heart left ventricleUBERON:000208486.67gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047386.30gold quality
cardiac ventricleUBERON:000208286.08gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451185.24silver quality
descending thoracic aortaUBERON:000234585.05gold quality
aortaUBERON:000094784.93gold quality
placentaUBERON:000198784.70gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-11268yes1960.23
E-ANND-3yes11.36
E-GEOD-36552no58.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

74 targeting EGFLAM, 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-7110-3P100.0073.182486
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-4692100.0067.322066
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-33A-5P99.9968.621055
HSA-MIR-33B-5P99.9968.581062
HSA-MIR-118499.9968.191458
HSA-MIR-451499.9967.101870
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-548N99.9871.944170
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-218-5P99.9372.222103
HSA-MIR-806399.9169.763146
HSA-MIR-329-3P99.9166.561234
HSA-MIR-362-3P99.9166.381267
HSA-MIR-63699.8069.581500
HSA-MIR-6817-3P99.7968.352126
HSA-MIR-4755-5P99.7170.342716
HSA-MIR-5006-3P99.7170.262728
HSA-MIR-128399.6972.423009
HSA-MIR-46699.6770.852863
HSA-MIR-320299.6667.702737
HSA-MIR-1212399.5271.792990
HSA-MIR-516A-3P99.4667.961378
HSA-MIR-516B-3P99.4667.961378
HSA-MIR-7162-5P99.4668.081368

Literature-anchored findings (GeneRIF, showing 5)

  • Strong candidate gene for macular dystrophy, MCDR3 (human 5p15.33-p13.1). Conclusion is based on a massive expression data set for mouse (103 strains) and joint analysis of RetNet database. (PMID:19727342)
  • rs1465567 of EGFLAM and rs113710653 of SPATC1L may be susceptibility loci for true aortic aneurysm and rs143881017 of RNASE13 may be such a locus for dissecting aortic aneurysm in Japanese individuals. (PMID:28339009)
  • this is the first report to describe that EGFLAM promoted the proliferation, migration and invasion of GBM cells via the activation of PI3K/AKT pathway, and predicted poor prognosis in GBM patients. (PMID:30829611)
  • Structure of the photoreceptor synaptic assembly of the extracellular matrix protein pikachurin with the orphan receptor GPR179. (PMID:37490546)
  • EGFLAM exhibits oncogenic activity and shows promise as a prognostic biomarker and therapeutic target in glioblastoma. (PMID:38996666)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioEGFLAMENSDARG00000099008
mus_musculusEgflamENSMUSG00000042961
rattus_norvegicusEgflamENSRNOG00000012058

Paralogs (27): USH2A (ENSG00000042781), LAMC3 (ENSG00000050555), LAMA3 (ENSG00000053747), LAMC2 (ENSG00000058085), NTN1 (ENSG00000065320), NTN4 (ENSG00000074527), ATRN (ENSG00000088812), LAMB4 (ENSG00000091128), LAMB1 (ENSG00000091136), LAMA1 (ENSG00000101680), MEGF8 (ENSG00000105429), MEGF9 (ENSG00000106780), ATRNL1 (ENSG00000107518), LAMA4 (ENSG00000112769), LAMA5 (ENSG00000130702), LAMC1 (ENSG00000135862), NTN5 (ENSG00000142233), HSPG2 (ENSG00000142798), TMEFF2 (ENSG00000144339), NTN3 (ENSG00000162068), NTNG1 (ENSG00000162631), LAMB2 (ENSG00000172037), AGRN (ENSG00000188157), NTNG2 (ENSG00000196358), LAMA2 (ENSG00000196569), LAMB3 (ENSG00000196878), TMEFF1 (ENSG00000241697)

Protein

Protein identifiers

PikachurinQ63HQ2 (reviewed: Q63HQ2)

Alternative names: Agrin-like protein, EGF-like, fibronectin type-III and laminin G-like domain-containing protein

All UniProt accessions (3): D6RG24, D6RJD2, Q63HQ2

UniProt curated annotations — full annotation on UniProt →

Function. Involved in both the retinal photoreceptor ribbon synapse formation and physiological functions of visual perception. Plays a key role in the synaptic organization of photoreceptors by mediating transsynaptic interaction between alpha-dystroglycan and GPR179 on the postsynaptic membrane. Necessary for proper bipolar dendritic tip apposition to the photoreceptor ribbon synapse. Promotes matrix assembly and cell adhesiveness.

Subunit / interactions. Interacts with DAG1 alpha-dystroglycan. Interacts with GPR158 and GPR179; transsynaptic interaction is required for synaptic organization of photoreceptor cells.

Subcellular location. Secreted. Extracellular space. Extracellular matrix. Synaptic cleft. Presynaptic active zone.

Post-translational modifications. O-glycosylated; contains chondroitin sulfate and heparan sulfate.

Isoforms (5)

UniProt IDNamesCanonical?
Q63HQ2-11yes
Q63HQ2-22
Q63HQ2-33
Q63HQ2-44
Q63HQ2-55

RefSeq proteins (4): NP_001192230, NP_689616, NP_877950, NP_877953 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000742EGFDomain
IPR001791Laminin_GDomain
IPR001881EGF-like_Ca-bd_domDomain
IPR003961FN3_domDomain
IPR013320ConA-like_dom_sfHomologous_superfamily
IPR013783Ig-like_foldHomologous_superfamily
IPR036116FN3_sfHomologous_superfamily
IPR050372Neurexin-related_CASPFamily
IPR056943EGF_PikachurinDomain

Pfam: PF00008, PF00041, PF00054, PF02210, PF25016

UniProt features (74 total): strand 29, disulfide bond 11, domain 8, sequence variant 6, splice variant 5, sequence conflict 5, turn 4, helix 3, signal peptide 1, chain 1, glycosylation site 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
7ZC9X-RAY DIFFRACTION2.1
7ZCBX-RAY DIFFRACTION2.5
8D1BELECTRON MICROSCOPY3.57

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q63HQ2-F180.810.51

Functional residue map

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

Disulfide bonds (11): 347–358, 352–369, 371–380, 534–564, 569–580, 574–590, 592–601, 788–799, 793–808, 810–819, 987–1014

Glycosylation sites (1): 47

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 119 (showing top): RNGTGGGC_UNKNOWN, AGGAAGC_MIR5163P, BENPORATH_ES_WITH_H3K27ME3, GGTGTGT_MIR329, WWTAAGGC_UNKNOWN, GOBP_SYNAPSE_ASSEMBLY, RORA1_01, TTTGTAG_MIR520D, CACCAGC_MIR138, AAAYRNCTG_UNKNOWN, GOBP_POSITIVE_REGULATION_OF_CELL_ADHESION, GOBP_CELL_JUNCTION_ORGANIZATION, SOX9_B1, GATA1_04, GATA1_03

GO Biological Process (3): synapse assembly (GO:0007416), positive regulation of cell-substrate adhesion (GO:0010811), extracellular matrix organization (GO:0030198)

GO Molecular Function (3): calcium ion binding (GO:0005509), glycosaminoglycan binding (GO:0005539), protein binding (GO:0005515)

GO Cellular Component (10): basement membrane (GO:0005604), interstitial matrix (GO:0005614), synaptic cleft (GO:0043083), presynaptic active zone (GO:0048786), photoreceptor ribbon synapse (GO:0098684), extracellular region (GO:0005576), cell surface (GO:0009986), extracellular matrix (GO:0031012), cell projection (GO:0042995), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
extracellular matrix2
nervous system development1
cell junction assembly1
synapse organization1
regulation of cell-substrate adhesion1
cell-substrate adhesion1
positive regulation of cell adhesion1
extracellular structure organization1
external encapsulating structure organization1
metal ion binding1
carbohydrate derivative binding1
binding1
extracellular region1
presynapse1
ribbon synapse1
external encapsulating structure1
cell junction1

Protein interactions and networks

STRING

2000 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EGFLAMDAG1Q14118994
EGFLAMDMDP11532690
EGFLAMPOMT2Q9UKY4649
EGFLAMPOMT1Q9Y6A1644
EGFLAMGPR179Q6PRD1628
EGFLAMCTBP2P56545617
EGFLAMCABP4P57796594
EGFLAMPOMGNT1Q8WZA1594
EGFLAMFKTNO75072592
EGFLAMTLR3O15455569
EGFLAMFKRPQ9H9S5547
EGFLAMNRXN2Q9P2S2541
EGFLAMB4GAT1O43505537
EGFLAMNRXN1Q9ULB1530
EGFLAMLRIT3Q3SXY7517

IntAct

10 interactions, top by confidence:

ABTypeScore
PDPK1AGRNpsi-mi:“MI:0914”(association)0.530
FGF1SDC4psi-mi:“MI:0914”(association)0.530
GPR179EGFLAMpsi-mi:“MI:0915”(physical association)0.460
GPR179EGFLAMpsi-mi:“MI:0403”(colocalization)0.460
CUL2ANXA2P2psi-mi:“MI:0914”(association)0.350
Gpr158AGRNpsi-mi:“MI:0914”(association)0.350
EGFLAMCLSTN1psi-mi:“MI:0914”(association)0.350
BTRCBHLHE40psi-mi:“MI:0914”(association)0.350

BioGRID (17): EGFLAM (Affinity Capture-RNA), EGFLAM (Affinity Capture-MS), EGFLAM (Affinity Capture-MS), EGFLAM (Affinity Capture-MS), EGFLAM (Affinity Capture-MS), EGFLAM (Affinity Capture-MS), FBXW11 (Affinity Capture-MS), EGFLAM (Affinity Capture-MS), DAG1 (Affinity Capture-MS), HSPA5 (Affinity Capture-MS), BTRC (Affinity Capture-MS), UBR1 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), MAN2C1 (Affinity Capture-MS), EGFLAM (Affinity Capture-MS)

ESM2 similar proteins: A1XQX0, A1XQX2, A1XQX8, A1XQY1, A3KN33, B4F785, B8UU78, D0PRN3, E9Q7X7, P12080, P29319, P29320, P54764, Q02763, Q02858, Q03137, Q06807, Q07310, Q07496, Q0V8S9, Q0V8T0, Q0V8T3, Q0V8T4, Q0V8T5, Q0V8T6, Q0V8T7, Q0V8T8, Q0V8T9, Q19617, Q28146, Q3KN41, Q4VBE4, Q5RD64, Q63372, Q63374, Q63HQ2, Q6P9K9, Q8QFX6, Q8WYK1, Q91694

Diamond homologs: A2ASQ1, A2ASS6, A3KN33, A8DYP0, B4F785, O00468, O35474, O43854, O55005, O88516, O89026, O94779, P00740, P25304, P29294, P35590, Q05793, Q06561, Q16787, Q4LDE5, Q4VBE4, Q5R7K9, Q5RBN1, Q63HQ2, Q7TPD3, Q8N9C0, Q8TER0, Q8WZ42, Q95ND7, Q96MS0, Q9HCK4, Q9NYJ7, Q9NYQ8, Q9Y2H6, Q9Y6N7, Q9Z2I4, A2CG49, G5EBF1, O01761, O60229

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance164
Likely benign9
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

4402 predictions. Top by Δscore:

VariantEffectΔscore
5:38258850:AGGTA:Adonor_loss1.0000
5:38258851:GGTAA:Gdonor_loss1.0000
5:38337511:T:TAacceptor_gain1.0000
5:38337512:G:Aacceptor_gain1.0000
5:38337630:G:GGdonor_gain1.0000
5:38338782:G:GAdonor_loss1.0000
5:38338783:T:TCdonor_loss1.0000
5:38338784:GA:Gdonor_loss1.0000
5:38370285:A:AGacceptor_gain1.0000
5:38370286:A:Gacceptor_gain1.0000
5:38370289:A:AGacceptor_gain1.0000
5:38370290:A:AGacceptor_gain1.0000
5:38370292:A:AGacceptor_gain1.0000
5:38370292:AAAG:Aacceptor_gain1.0000
5:38370293:A:Gacceptor_gain1.0000
5:38370294:A:AGacceptor_gain1.0000
5:38370295:G:GGacceptor_gain1.0000
5:38370295:GGCC:Gacceptor_gain1.0000
5:38370295:GGCCA:Gacceptor_gain1.0000
5:38370463:G:GGdonor_gain1.0000
5:38406121:T:TAacceptor_gain1.0000
5:38406124:A:AGacceptor_gain1.0000
5:38406125:G:GGacceptor_gain1.0000
5:38406237:AGGAG:Adonor_loss1.0000
5:38406238:GGAG:Gdonor_gain1.0000
5:38406238:GGAGG:Gdonor_loss1.0000
5:38406239:G:GTdonor_gain1.0000
5:38406240:AGGT:Adonor_loss1.0000
5:38406241:GGT:Gdonor_loss1.0000
5:38406243:T:Gdonor_loss1.0000

AlphaMissense

6630 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:38352270:T:AW162R0.994
5:38352270:T:CW162R0.994
5:38458382:T:AV928D0.993
5:38431215:T:CL698P0.992
5:38427183:T:CL662P0.991
5:38431227:G:CR702P0.991
5:38458372:T:AW925R0.991
5:38458372:T:CW925R0.991
5:38407901:T:CF415S0.990
5:38425050:T:CC590R0.990
5:38448349:T:CL846P0.990
5:38370391:T:CF214S0.989
5:38425056:T:CC592R0.989
5:38427216:T:CF673S0.989
5:38427219:G:CR674P0.989
5:38451382:T:AW879R0.989
5:38451382:T:CW879R0.989
5:38458388:C:AA930D0.989
5:38425052:C:GC590W0.988
5:38425083:T:AC601S0.988
5:38425084:G:CC601S0.988
5:38427185:T:CS663P0.988
5:38458374:G:CW925C0.988
5:38458374:G:TW925C0.988
5:38462985:T:CL958P0.988
5:38337585:T:AW55R0.987
5:38337585:T:CW55R0.987
5:38425084:G:AC601Y0.987
5:38438419:T:CC810R0.987
5:38407895:T:CL413P0.986

dbSNP variants (sampled 300 via entrez): RS1000031020 (5:38354703 C>T), RS1000040573 (5:38369994 G>C), RS1000058290 (5:38296743 G>A), RS1000076544 (5:38415839 G>A), RS1000078375 (5:38342926 C>G), RS1000108875 (5:38462762 T>C,G), RS1000112961 (5:38418466 G>A), RS1000137512 (5:38399432 T>C), RS1000167522 (5:38289604 T>G), RS1000174045 (5:38352812 G>C,T), RS1000178226 (5:38294562 T>C), RS1000203315 (5:38373217 T>G), RS1000210679 (5:38334995 C>T), RS1000211303 (5:38337874 A>C), RS1000267842 (5:38399952 C>A,T)

Disease associations

OMIM: gene MIM:617683 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST001591_1Response to citalopram treatment3.000000e-06
GCST003801_5Response to selective serotonin reuptake inhibitors in depression4.000000e-07
GCST005174_17Coronary artery calcified atherosclerotic plaque score in type 2 diabetes6.000000e-06
GCST005212_31Asthma3.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0005658response to selective serotonin reuptake inhibitor
EFO:0004723coronary artery calcification

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression4
Benzo(a)pyreneaffects methylation, increases expression3
bisphenol Adecreases methylation, affects cotreatment, increases expression2
Vorinostataffects cotreatment, increases expression2
Dexamethasoneincreases expression, affects cotreatment2
bisphenol Faffects cotreatment, increases expression1
ethyl-p-hydroxybenzoateincreases expression1
trichostatin Aincreases expression1
arseniteincreases methylation1
mono-(2-ethylhexyl)phthalateincreases abundance, increases methylation1
tebuconazoledecreases expression1
entinostatincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
Acetaminophendecreases expression1
Arsenicaffects methylation1
Cytarabinedecreases expression1
Diethylhexyl Phthalateincreases abundance, increases methylation1
Doxorubicindecreases expression1
Indomethacinaffects cotreatment, increases expression1
Leadaffects expression1
Pesticidesdecreases methylation1
Rotenonedecreases expression1
Thiramdecreases expression1
Tretinoindecreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Cyclosporinedecreases methylation1
Aflatoxin B1affects methylation1
Okadaic Aciddecreases expression1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_A1F1SEES3-1V human EGFLAM, clone1Embryonic stem cellMale
CVCL_A1F2SEES3-1V human EGFLAM, clone2Embryonic stem cellMale
CVCL_A1F3SEES3-1V human EGFLAM, clone3Embryonic stem cellMale

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.