FRMD3

gene
On this page

Also known as EPB41L4OMGC20553

Summary

FRMD3 (FERM domain containing 3, HGNC:24125) is a protein-coding gene on chromosome 9q21.32, encoding FERM domain-containing protein 3 (A2A2Y4). Putative tumor suppressor gene that may be implicated in the origin and progression of lung cancer.

The protein encoded by this gene is a single pass membrane protein primarily found in ovaries. A similar protein in erythrocytes helps determine the shape of red blood cells, but the function of the encoded protein has not been determined. There is some evidence that this is a tumor suppressor gene, and there is also evidence linking defects in this gene to susceptibility to diabetic nephropathy in type 1 diabetes. Several transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 257019 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 92 total
  • MANE Select transcript: NM_174938

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24125
Approved symbolFRMD3
NameFERM domain containing 3
Location9q21.32
Locus typegene with protein product
StatusApproved
AliasesEPB41L4O, MGC20553
Ensembl geneENSG00000172159
Ensembl biotypeprotein_coding
OMIM607619
Entrez257019

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 10 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000304195, ENST00000328788, ENST00000376434, ENST00000376438, ENST00000431299, ENST00000465485, ENST00000621208, ENST00000874517, ENST00000874518, ENST00000874519, ENST00000962006

RefSeq mRNA: 6 — MANE Select: NM_174938 NM_001244959, NM_001244960, NM_001244961, NM_001244962, NM_001375487, NM_174938

CCDS: CCDS43840, CCDS59131, CCDS59132, CCDS59133, CCDS75852

Canonical transcript exons

ENST00000304195 — 14 exons

ExonStartEnd
ENSE000009176208333551683335639
ENSE000009829768334319083343287
ENSE000009829778331366083313747
ENSE000010904368329874883298816
ENSE000010904378329911283299186
ENSE000010904388330953683309624
ENSE000010904398329060383290727
ENSE000011979018331188783311975
ENSE000012146278331048583310548
ENSE000016724598337291383372955
ENSE000017326278334967983349757
ENSE000017517908338960483389708
ENSE000019393148324462283248516
ENSE000027291168353808583538401

Expression profiles

Bgee: expression breadth ubiquitous, 250 present calls, max score 99.91.

FANTOM5 (CAGE): breadth broad, TPM avg 4.2178 / max 256.9421, expressed in 843 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1011353.4914763
1011310.4532111
1011320.2600119
1011300.01334

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065599.91gold quality
kidney epitheliumUBERON:000481996.86gold quality
left ventricle myocardiumUBERON:000656696.69gold quality
apex of heartUBERON:000209896.01gold quality
oocyteCL:000002395.41gold quality
cardiac muscle of right atriumUBERON:000337994.93gold quality
myocardiumUBERON:000234994.69gold quality
ileal mucosaUBERON:000033194.42gold quality
cardiac ventricleUBERON:000208294.01gold quality
heart left ventricleUBERON:000208494.01gold quality
muscle of legUBERON:000138393.11gold quality
gastrocnemiusUBERON:000138893.07gold quality
skeletal muscle organUBERON:001489292.81gold quality
cortical plateUBERON:000534392.75gold quality
heart right ventricleUBERON:000208092.71gold quality
seminal vesicleUBERON:000099892.56gold quality
hindlimb stylopod muscleUBERON:000425292.45gold quality
deltoidUBERON:000147692.19gold quality
tibialis anteriorUBERON:000138591.89gold quality
biceps brachiiUBERON:000150791.89gold quality
quadriceps femorisUBERON:000137791.85gold quality
vastus lateralisUBERON:000137991.80gold quality
trigeminal ganglionUBERON:000167591.71gold quality
epithelial cell of pancreasCL:000008391.24silver quality
dorsal root ganglionUBERON:000004491.09gold quality
skeletal muscle tissueUBERON:000113491.07gold quality
corpus epididymisUBERON:000435991.00gold quality
cardiac atriumUBERON:000208190.82gold quality
heartUBERON:000094890.81gold quality
caput epididymisUBERON:000435890.68gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-MTAB-11268yes2174.48
E-CURD-119yes43.27
E-MTAB-7249yes39.48
E-MTAB-7316yes22.96
E-ANND-3yes10.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

134 targeting FRMD3, 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-6867-5P100.0082.213464
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-8485100.0077.574731
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-656-3P100.0072.152788
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-428299.9975.366408
HSA-MIR-548C-3P99.9974.017587
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-4715-3P99.9866.03670
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-548AN99.9770.912817
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-493-5P99.9672.472382
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-1-3P99.9372.351914
HSA-MIR-20699.9372.501893
HSA-MIR-145-5P99.9271.131836
HSA-MIR-5195-3P99.9270.921877

Literature-anchored findings (GeneRIF, showing 6)

  • identify FRMD3 as a novel putative tumour suppressor gene suggesting an important role in the origin and progression of lung cancer. (PMID:17260017)
  • These analyses reveal a role for FRMD3 in AA T2DN susceptibility. (PMID:21698141)
  • model for FRMD3 in diabetic nephropathy proposes a possible transcriptional link through which the polymorphism in the FRMD3 promoter could influence transcriptional regulation within the bone morphogenetic protein (BMP)-signaling pathway (PMID:23434934)
  • The risk (G and C) and non-risk (C and T) allele frequencies of the SNPs at the rs1888747 and rs739401 loci of FRMD3 and CARS, respectively, did not differ significantly between the diabetics with (case) and without (control) nephropathy (P > 0.05). (PMID:26909942)
  • Hsa-miR-3651 could serve as a novel predictor for in-breast recurrence via FRMD3. (PMID:34865205)
  • FRMD3 inhibits the growth and metastasis of breast cancer through the ubiquitination-mediated degradation of vimentin and subsequent impairment of focal adhesion. (PMID:36631457)

Cross-species orthologs

10 orthologs

OrganismSymbolGene ID
danio_reriofrmd3ENSDARG00000059885
mus_musculusFrmd3ENSMUSG00000049122
rattus_norvegicusFrmd3ENSRNOG00000006503
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), EPB41 (ENSG00000159023), FRMD5 (ENSG00000171877)

Protein

Protein identifiers

FERM domain-containing protein 3A2A2Y4 (reviewed: A2A2Y4)

Alternative names: Band 4.1-like protein 4O, Ovary type protein 4.1

All UniProt accessions (2): A2A2Y4, Q5JV61

UniProt curated annotations — full annotation on UniProt →

Function. Putative tumor suppressor gene that may be implicated in the origin and progression of lung cancer.

Subcellular location. Membrane.

Tissue specificity. Ovary-specific.

Isoforms (5)

UniProt IDNamesCanonical?
A2A2Y4-11yes
A2A2Y4-22
A2A2Y4-33
A2A2Y4-44
A2A2Y4-55

RefSeq proteins (6): NP_001231888, NP_001231889, NP_001231890, NP_001231891, NP_001362416, NP_777598* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000299FERM_domainDomain
IPR000798Ez/rad/moesin-likeFamily
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
IPR029071Ubiquitin-like_domsfHomologous_superfamily
IPR035963FERM_2Homologous_superfamily

Pfam: PF00373, PF08736, PF09379, PF09380

UniProt features (13 total): splice variant 6, sequence conflict 2, chain 1, transmembrane region 1, sequence variant 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A2A2Y4-F175.030.45

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 139 (showing top): BENPORATH_ES_WITH_H3K27ME3, RODWELL_AGING_KIDNEY_NO_BLOOD_DN, TGIF_01, GOBP_ACTOMYOSIN_STRUCTURE_ORGANIZATION, CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP, chr9q21, GOMF_CYTOSKELETAL_PROTEIN_BINDING, HORIUCHI_WTAP_TARGETS_UP, GSE14415_INDUCED_TREG_VS_FOXP3_KO_INDUCED_TREG_IL2_CULTURE_DN, HMGA1_TARGET_GENES, HOXC6_TARGET_GENES, LHX9_TARGET_GENES, TFEB_TARGET_GENES, ZIM3_TARGET_GENES, ZNF22_TARGET_GENES

GO Biological Process (1): actomyosin structure organization (GO:0031032)

GO Molecular Function (2): cytoskeletal protein binding (GO:0008092), protein binding (GO:0005515)

GO Cellular Component (2): cytoskeleton (GO:0005856), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
actin cytoskeleton organization1
protein binding1
binding1
intracellular membraneless organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

482 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FRMD3CPVLQ9H3G5668
FRMD3A0A2R8YEI5A0A2R8YEI5663
FRMD3LRRIQ3A6PVS8645
FRMD3MYH9P35579628
FRMD3RASEFQ8IZ41622
FRMD3CHN2P52757621
FRMD3SAMD5Q5TGI4616
FRMD3TMC7Q7Z402612
FRMD3NIBAN3Q86XR2596
FRMD3ELMO1Q92556571
FRMD3CNDP1Q96KN2542
FRMD3C1orf94Q6P1W5518
FRMD3CARS1P49589507
FRMD3CARS2Q9HA77501
FRMD3MS4A1P08984488

IntAct

42 interactions, top by confidence:

ABTypeScore
FRMD3ZFPL1psi-mi:“MI:0915”(physical association)0.560
FRMD3PLPP4psi-mi:“MI:0915”(physical association)0.560
FRMD3CMTM7psi-mi:“MI:0915”(physical association)0.560
FRMD3TMEM97psi-mi:“MI:0915”(physical association)0.560
FRMD3JAGN1psi-mi:“MI:0915”(physical association)0.560
FRMD3TMEM201psi-mi:“MI:0915”(physical association)0.560
FRMD3SERP2psi-mi:“MI:0915”(physical association)0.560
FRMD3TMEM218psi-mi:“MI:0915”(physical association)0.560
FRMD3SERP1psi-mi:“MI:0915”(physical association)0.560
FRMD3NRMpsi-mi:“MI:0915”(physical association)0.560
FRMD3SLC35A4psi-mi:“MI:0915”(physical association)0.560
FRMD3CYB5Bpsi-mi:“MI:0915”(physical association)0.560
nleA/espIFRMD3psi-mi:“MI:0915”(physical association)0.370
FRMD3nleA/espIpsi-mi:“MI:0915”(physical association)0.370
FRMD3FAM234Bpsi-mi:“MI:0914”(association)0.350
NFIBpsi-mi:“MI:0914”(association)0.350
FRMD3ATP5F1Dpsi-mi:“MI:0914”(association)0.350
ZFPL1FRMD3psi-mi:“MI:0915”(physical association)0.000
TMEM218FRMD3psi-mi:“MI:0915”(physical association)0.000
SERP1FRMD3psi-mi:“MI:0915”(physical association)0.000
NRMFRMD3psi-mi:“MI:0915”(physical association)0.000
SLC35A4FRMD3psi-mi:“MI:0915”(physical association)0.000
CYB5BFRMD3psi-mi:“MI:0915”(physical association)0.000
PLPP4FRMD3psi-mi:“MI:0915”(physical association)0.000
CMTM7FRMD3psi-mi:“MI:0915”(physical association)0.000
TMEM97FRMD3psi-mi:“MI:0915”(physical association)0.000
JAGN1FRMD3psi-mi:“MI:0915”(physical association)0.000
TMEM201FRMD3psi-mi:“MI:0915”(physical association)0.000

BioGRID (33): ATP5D (Affinity Capture-MS), ATP5O (Affinity Capture-MS), OXA1L (Affinity Capture-MS), COLEC12 (Affinity Capture-MS), LCLAT1 (Affinity Capture-MS), KLHL15 (Affinity Capture-MS), REEP4 (Affinity Capture-MS), KIAA1467 (Affinity Capture-MS), GYLTL1B (Affinity Capture-MS), CKAP4 (Affinity Capture-MS), LMBR1 (Affinity Capture-MS), FRMD3 (Affinity Capture-RNA), FRMD3 (Two-hybrid), FRMD3 (Two-hybrid), FRMD3 (Two-hybrid)

ESM2 similar proteins: A0JM95, A1A4S6, A2A2Y4, A4II46, A4IJ06, A6NI28, B2RQE8, B5DFQ4, F1LVW7, O60879, O60890, O70566, O95267, P0C7A6, P0CAX5, Q02384, Q07889, Q07890, Q08DP6, Q0P4Q4, Q28EC1, Q4V7P7, Q566W7, Q5R6F6, Q5R803, Q5U4T3, Q62245, Q69ZK0, Q6DBW1, Q6DHR3, Q6NTL4, Q6PCS4, Q6Y5D8, Q6ZM89, Q7YQL5, Q7YQL6, Q8AVG0, Q8BHD4, Q8IV61, Q8N9B8

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

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance67
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3986 predictions. Top by Δscore:

VariantEffectΔscore
9:83248134:CTTG:Cdonor_gain1.0000
9:83248136:TG:Tdonor_gain1.0000
9:83248402:T:TAdonor_gain1.0000
9:83248417:T:TAdonor_gain1.0000
9:83290597:ACTT:Adonor_loss1.0000
9:83290598:CTT:Cdonor_loss1.0000
9:83290599:TTA:Tdonor_loss1.0000
9:83290600:TA:Tdonor_loss1.0000
9:83290601:A:ACdonor_gain1.0000
9:83290601:AC:Adonor_gain1.0000
9:83290601:ACCC:Adonor_loss1.0000
9:83290602:C:CCdonor_gain1.0000
9:83290602:CC:Cdonor_gain1.0000
9:83290602:CCCT:Cdonor_gain1.0000
9:83290726:CT:Cacceptor_gain1.0000
9:83290727:TCTG:Tacceptor_loss1.0000
9:83290728:C:CCacceptor_gain1.0000
9:83290728:CTGA:Cacceptor_loss1.0000
9:83290729:T:Gacceptor_loss1.0000
9:83298743:CTCA:Cdonor_loss1.0000
9:83298745:CA:Cdonor_loss1.0000
9:83298746:A:ATdonor_loss1.0000
9:83298747:C:Gdonor_loss1.0000
9:83298812:TCCCA:Tacceptor_gain1.0000
9:83298813:CCCA:Cacceptor_gain1.0000
9:83298813:CCCAC:Cacceptor_gain1.0000
9:83298814:CCA:Cacceptor_gain1.0000
9:83298814:CCAC:Cacceptor_gain1.0000
9:83298815:CA:Cacceptor_gain1.0000
9:83298815:CAC:Cacceptor_gain1.0000

AlphaMissense

3966 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:83309570:A:GW298R1.000
9:83309570:A:TW298R1.000
9:83309572:A:GL297P1.000
9:83309580:G:CC294W1.000
9:83309581:C:TC294Y1.000
9:83311888:A:GW258R1.000
9:83311888:A:TW258R1.000
9:83311947:C:TG238E1.000
9:83313663:G:CC227W1.000
9:83313671:G:CH225D1.000
9:83343240:A:GL141P1.000
9:83343243:C:GR140P1.000
9:83343258:T:AD135V1.000
9:83343258:T:GD135A1.000
9:83343259:C:GD135H1.000
9:83349720:G:CF111L1.000
9:83349720:G:TF111L1.000
9:83349722:A:GF111L1.000
9:83372948:A:GL87P1.000
9:83372948:A:TL87H1.000
9:83372950:C:AW86C1.000
9:83372950:C:GW86C1.000
9:83372952:A:GW86R1.000
9:83372952:A:TW86R1.000
9:83389696:C:AG54W1.000
9:83309541:A:CF307L0.999
9:83309541:A:TF307L0.999
9:83309542:A:GF307S0.999
9:83309543:A:GF307L0.999
9:83309560:C:TG301E0.999

dbSNP variants (sampled 300 via entrez): RS1000014571 (9:83498251 T>C), RS1000028099 (9:83344954 T>C), RS1000037327 (9:83307830 A>G,T), RS1000049751 (9:83286588 T>C), RS1000050735 (9:83475857 C>T), RS1000050976 (9:83562468 C>T), RS1000066898 (9:83485971 T>C), RS1000084306 (9:83436440 CA>C), RS1000086053 (9:83568172 CT>C), RS1000103296 (9:83388306 G>C), RS1000113120 (9:83451817 C>T), RS1000116725 (9:83258879 A>C,T), RS1000128851 (9:83319865 G>A,T), RS1000134759 (9:83442547 A>G), RS1000135898 (9:83265301 G>A)

Disease associations

OMIM: gene MIM:607619 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

StudyTraitp-value
GCST002591_22Lewy body disease9.000000e-06
GCST002591_40Lewy body disease2.000000e-06
GCST003773_8Loneliness (multivariate analysis)4.000000e-07
GCST004384_4Hypertension1.000000e-08
GCST004388_1Blood pressure traits (multi-trait analysis)7.000000e-09
GCST005221_1Insulin sensitivity index2.000000e-07
GCST009391_2131Metabolite levels6.000000e-06

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0006799Lewy body dementia measurement
EFO:0007865loneliness measurement
EFO:0005763pulse pressure measurement
EFO:0006335systolic blood pressure
EFO:0006336diastolic blood pressure
EFO:0004471insulin sensitivity measurement
EFO:0010383phosphatidylcholine 36:5 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression5
mercuric bromidedecreases expression, affects cotreatment2
Air Pollutantsincreases expression, decreases expression2
Benzo(a)pyrenedecreases expression2
Estradiolaffects cotreatment, decreases expression, increases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Cyclosporinedecreases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, decreases expression2
aristolochic acid Idecreases expression1
FR900359decreases phosphorylation1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, increases activity, increases expression1
bisphenol Adecreases expression1
2,5,2’,5’-tetrachlorobiphenylincreases expression1
trichostatin Aincreases expression1
arseniteincreases methylation1
mono-(2-ethylhexyl)phthalateincreases expression1
sodium arseniteaffects splicing, decreases expression1
ochratoxin Aincreases expression1
aflatoxin B2increases methylation1
nickel sulfateincreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression, increases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression, increases expression1
MRK 003decreases expression1
bisphenol Saffects cotreatment, decreases methylation1
jinfukangaffects cotreatment, increases expression1
gardiquimodincreases expression, decreases reaction1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Lewy body dementia