FRMPD2

gene
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Also known as MGC35285

Summary

FRMPD2 (FERM and PDZ domain containing 2, HGNC:28572) is a protein-coding gene on chromosome 10q11.22, encoding FERM and PDZ domain-containing protein 2 (Q68DX3). Functions as a scaffold protein and likely plays a role in N-methyl-D-aspartic acid receptor (NMDAR)-mediated synaptic excitatory transmission.

This gene encodes a peripheral membrane protein and is located in a region of chromosome 10q that contains a segmental duplication. This copy of the gene is full-length and is in the telomeric duplicated region. Two other more centromerically proximal copies of the gene are partial and may represent pseudogenes. This full-length gene appears to function in the establishment and maintenance of cell polarization. The protein is recruited to cell-cell junctions in an E-cadherin-dependent manner, and is selectively localized at the basolateral membrane in polarized epithelial cells. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 143162 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 207 total
  • MANE Select transcript: NM_001018071

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28572
Approved symbolFRMPD2
NameFERM and PDZ domain containing 2
Location10q11.22
Locus typegene with protein product
StatusApproved
AliasesMGC35285
Ensembl geneENSG00000170324
Ensembl biotypeprotein_coding
OMIM613323
Entrez143162

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 7 retained_intron, 3 protein_coding, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000305531, ENST00000374201, ENST00000463706, ENST00000468556, ENST00000474573, ENST00000477710, ENST00000486151, ENST00000491130, ENST00000492045, ENST00000494505, ENST00000505547, ENST00000635925, ENST00000636244, ENST00000637395

RefSeq mRNA: 3 — MANE Select: NM_001018071 NM_001018071, NM_001042512, NM_001318191

CCDS: CCDS31195, CCDS81460

Canonical transcript exons

ENST00000374201 — 29 exons

ExonStartEnd
ENSE000016318024822231348222451
ENSE000017029104821195448212109
ENSE000017263334822312348223270
ENSE000018833944827454348274696
ENSE000024637464817804748178151
ENSE000024922314815656248157370
ENSE000034694694816859548168693
ENSE000034782104824036048240492
ENSE000034974844819268448192894
ENSE000035267054823648248236553
ENSE000035296624817487048174955
ENSE000035315824825156648251691
ENSE000035316024820122848201384
ENSE000035388424817099448171208
ENSE000035518274818477448184881
ENSE000035644314820674848206933
ENSE000035783724818456648184682
ENSE000035902964824902148249178
ENSE000035921624817584648175939
ENSE000035991844816332848163671
ENSE000036177354817294648173093
ENSE000036255504818555348185645
ENSE000036353494823960548239692
ENSE000036410744823211548232289
ENSE000036723724824478448244849
ENSE000036734414824216148242352
ENSE000036780924818080348181008
ENSE000036803034823799148238123
ENSE000036916974818719248187292

Expression profiles

Bgee: expression breadth ubiquitous, 127 present calls, max score 93.17.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.9917 / max 164.6851, expressed in 173 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter IDTPM avgSamples expressed
1092910.4176107
1092940.243549
1092950.157251
1092930.056216
1092920.051417
1092880.030510
1092870.01724
1092900.01614
1092890.00200

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
superior frontal gyrusUBERON:000266193.17gold quality
quadriceps femorisUBERON:000137787.31gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.29gold quality
dorsolateral prefrontal cortexUBERON:000983486.03gold quality
Brodmann (1909) area 9UBERON:001354085.82gold quality
right frontal lobeUBERON:000281085.21gold quality
anterior cingulate cortexUBERON:000983584.47gold quality
frontal cortexUBERON:000187083.34gold quality
right uterine tubeUBERON:000130283.17gold quality
olfactory segment of nasal mucosaUBERON:000538683.03gold quality
cerebral cortexUBERON:000095682.15gold quality
corpus callosumUBERON:000233682.05gold quality
prefrontal cortexUBERON:000045181.29gold quality
primary visual cortexUBERON:000243679.21gold quality
telencephalonUBERON:000189378.73gold quality
left testisUBERON:000453377.73gold quality
hypothalamusUBERON:000189877.63gold quality
temporal lobeUBERON:000187177.47gold quality
amygdalaUBERON:000187677.27gold quality
testisUBERON:000047377.25gold quality
right testisUBERON:000453476.88gold quality
caudate nucleusUBERON:000187376.81gold quality
brainUBERON:000095573.85gold quality
Ammon’s hornUBERON:000195473.49gold quality
nucleus accumbensUBERON:000188271.67gold quality
substantia nigraUBERON:000203868.90gold quality
fallopian tubeUBERON:000388967.56gold quality
putamenUBERON:000187466.77gold quality
right lungUBERON:000216764.44gold quality
right atrium auricular regionUBERON:000663162.95gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes10.71

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

  • These results provide novel insights into the molecular function of FRMPD2 and into the targeting mechanism of peripheral membrane proteins in polarized epithelial cells. (PMID:19706687)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriofrmpd2ENSDARG00000074119
mus_musculusFrmpd2ENSMUSG00000108841
rattus_norvegicusFrmpd2ENSRNOG00000029131
caenorhabditis_elegansWBGENE00001492
caenorhabditis_elegansWBGENE00021406

Paralogs (5): LNX1 (ENSG00000072201), MPDZ (ENSG00000107186), PATJ (ENSG00000132849), LNX2 (ENSG00000139517), STXBP4 (ENSG00000166263)

Protein

Protein identifiers

FERM and PDZ domain-containing protein 2Q68DX3 (reviewed: Q68DX3)

Alternative names: PDZ domain-containing protein 4, PDZ domain-containing protein 5C

All UniProt accessions (3): Q68DX3, A0A1B0GUQ4, A0A1B0GV40

UniProt curated annotations — full annotation on UniProt →

Function. Functions as a scaffold protein and likely plays a role in N-methyl-D-aspartic acid receptor (NMDAR)-mediated synaptic excitatory transmission. May be involved in synapse formation in cone photoreceptor cells. May play a role in the regulation of tight junction formation. Binds phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2). May play a role in the regulation of NOD2-mediated NF-kappa-B activation in immune response.

Subunit / interactions. Interacts (via the second PDZ domain) with CTNND2 (via the extreme C-terminus). Interacts (via the second PDZ domain) with PKP4 (via the extreme C-terminus); the interaction directs FRMPD2 to the basolateral membranes. Interacts (via the second PDZ domain) with ARVCF (via the extreme C-terminus). Interacts (via the second PDZ domain) with NMDAR subunits GRIN2A/GLUN2A and GRIN2B/GLUN2B (via the extreme C-terminus); the interaction is direct and is likely to promote NMDAR-mediated neural signal transmission. Interacts (via the third PDZ domain) with LRIT1 (via the extreme C-terminus); the interaction leads to their colocalization in photoreceptor synapses. Interacts with NOD2; the interaction is likely to trigger NOD2-mediated NF-kappa-B activation.

Subcellular location. Cytoplasm. Basolateral cell membrane. Cell junction. Tight junction. Postsynaptic density.

Tissue specificity. Expressed in epithelial cells.

Domain organisation. The FERM and PDZ 2 domains are necessary for localization to the basolateral cell membrane. The FERM domain binds to phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2) and is sufficient for membrane localization.

Isoforms (5)

UniProt IDNamesCanonical?
Q68DX3-11yes
Q68DX3-22
Q68DX3-33
Q68DX3-44
Q68DX3-55

RefSeq proteins (2): NP_001018081, NP_001305120 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000299FERM_domainDomain
IPR001478PDZDomain
IPR011019KIND_domDomain
IPR011993PH-like_dom_sfHomologous_superfamily
IPR014352FERM/acyl-CoA-bd_prot_sfHomologous_superfamily
IPR018979FERM_NDomain
IPR018980FERM_PH-like_CDomain
IPR019748FERM_centralDomain
IPR019749Band_41_domainDomain
IPR029071Ubiquitin-like_domsfHomologous_superfamily
IPR035963FERM_2Homologous_superfamily
IPR036034PDZ_sfHomologous_superfamily
IPR052074NonRcpt_TyrProt_PhosphataseFamily

Pfam: PF00373, PF00595, PF09379, PF09380

UniProt features (36 total): sequence conflict 9, splice variant 8, sequence variant 6, domain 5, region of interest 4, compositionally biased region 2, chain 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q68DX3-F164.040.27

Functional residue map

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

Mutagenesis-validated functional residues (1):

PositionPhenotype
955abolishes the basolateral membrane localization.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 58 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, GOBP_APICAL_JUNCTION_ASSEMBLY, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_CELL_JUNCTION_ASSEMBLY, GOBP_CELL_CELL_JUNCTION_ASSEMBLY, GOCC_CELL_CELL_JUNCTION, GOCC_APICAL_PART_OF_CELL, GOCC_POSTSYNAPSE, GOCC_SYNAPSE, CAMPS_COLON_CANCER_COPY_NUMBER_DN, GOCC_ANCHORING_JUNCTION, GOCC_PLASMA_MEMBRANE_REGION, GOCC_BASAL_PART_OF_CELL, GOMF_PHOSPHATIDYLINOSITOL_BINDING, GOMF_1_PHOSPHATIDYLINOSITOL_BINDING

GO Biological Process (1): bicellular tight junction assembly (GO:0070830)

GO Molecular Function (2): 1-phosphatidylinositol binding (GO:0005545), protein binding (GO:0005515)

GO Cellular Component (10): cytoplasm (GO:0005737), plasma membrane (GO:0005886), bicellular tight junction (GO:0005923), postsynaptic density (GO:0014069), basolateral plasma membrane (GO:0016323), apical part of cell (GO:0045177), cytoskeleton (GO:0005856), membrane (GO:0016020), synapse (GO:0045202), anchoring junction (GO:0070161)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
cell junction2
apical junction assembly1
tight junction assembly1
phospholipid binding1
binding1
intracellular anatomical structure1
membrane1
cell periphery1
apical junction complex1
tight junction1
asymmetric synapse1
postsynaptic specialization1
basal plasma membrane1
plasma membrane region1
intracellular membraneless organelle1

Protein interactions and networks

STRING

434 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FRMPD2PKP4Q99569804
FRMPD2ARVCFO00192755
FRMPD2CTNND2Q9UQB3699
FRMPD2CTNND1O60716597
FRMPD2PTPN20Q4JDL3533
FRMPD2REM1O75628460
FRMPD2ARHGAP22Q7Z5H3449
FRMPD2GDF10P55107443
FRMPD2AGAP6Q5VW22436
FRMPD2SNTA1Q13424435
FRMPD2UBTD1Q9HAC8434
FRMPD2PPP1R27Q86WC6427
FRMPD2KNDC1Q76NI1419
FRMPD2CDH1P12830415
FRMPD2FHIP2AQ5W0V3411

IntAct

1132 interactions, top by confidence:

ABTypeScore
PCGF5CSNK2A2psi-mi:“MI:0914”(association)0.880
FRMPD2NRXN3psi-mi:“MI:0407”(direct interaction)0.440
FRMPD2PTENpsi-mi:“MI:0407”(direct interaction)0.440
GAS2L2FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
ABCA1FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
DGKIFRMPD2psi-mi:“MI:0407”(direct interaction)0.440
TRPV3FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
MCM7FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
SLC1A7FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
EPHA7FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
RAPGEF2FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
ARHGAP6FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
DGKZFRMPD2psi-mi:“MI:0407”(direct interaction)0.440
PLEKHA1FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
RAPGEF6FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
CNKSR2FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
XKR7FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
FRMPD2FCHSD2psi-mi:“MI:0407”(direct interaction)0.440
RGS12FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
PBKFRMPD2psi-mi:“MI:0407”(direct interaction)0.440
PTPRZ1FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
HTR2AFRMPD2psi-mi:“MI:0407”(direct interaction)0.440
FRMPD2ATP2B4psi-mi:“MI:0407”(direct interaction)0.440
APCFRMPD2psi-mi:“MI:0407”(direct interaction)0.440
CTNND2FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
FRMPD2PTPRGpsi-mi:“MI:0407”(direct interaction)0.440
NECTIN3FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
KCNA7FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
SLC16A3FRMPD2psi-mi:“MI:0407”(direct interaction)0.440
FRMPD2PPFIA1psi-mi:“MI:0407”(direct interaction)0.440

BioGRID (19): PKN2 (Affinity Capture-MS), SARS (Affinity Capture-MS), PKN2 (Affinity Capture-MS), SARS (Affinity Capture-MS), FRMPD2 (Affinity Capture-RNA), FRMPD2 (Protein-peptide), E6 (PCA), PKN2 (Affinity Capture-MS), FRMPD2 (Affinity Capture-MS), SARS (Affinity Capture-MS), PROSC (Affinity Capture-MS), NAGK (Affinity Capture-MS), SLC25A31 (Affinity Capture-MS), LIMCH1 (Affinity Capture-MS), VPS37C (Affinity Capture-MS)

ESM2 similar proteins: A0A140LI67, B5KFD7, D4A7V9, M0R4F8, O08774, O35827, O43187, O70167, O70173, O88866, O88900, O95398, O95704, P0C5Y8, Q0P5I2, Q13322, Q14449, Q4QQS0, Q5BIW4, Q5ICW4, Q5JV73, Q5PQS0, Q5R810, Q60760, Q68DX3, Q6IFT4, Q6IRN0, Q6P4K6, Q6REY9, Q6S5L8, Q6TXD4, Q7TSI1, Q80TQ5, Q80VA5, Q8BW88, Q8CFA1, Q8IWE5, Q8R1C9, Q8R2S1, Q8VCC8

Diamond homologs: A0A140LI67, A5PKA5, A7UA95, E1JIT7, O14910, O15018, O19132, O35274, O35867, O35889, O62666, O62674, O62675, O62676, O62677, O62678, O88951, O88952, P11434, P29475, P29476, P31016, P51140, P55196, P57105, P78352, Q07436, Q0P5F3, Q12923, Q14005, Q29498, Q2KIB6, Q32LM6, Q3T0C9, Q3UHD6, Q4KL35, Q5F425, Q5RAA5, Q62108, Q64512

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 115 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
EPHB-mediated forward signaling516.4×7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance168
Likely benign26
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

5101 predictions. Top by Δscore:

VariantEffectΔscore
10:48174865:CTCA:Cdonor_loss1.0000
10:48174866:TCA:Tdonor_loss1.0000
10:48174867:CAC:Cdonor_loss1.0000
10:48174868:ACCTG:Adonor_gain1.0000
10:48174869:C:CGdonor_loss1.0000
10:48174869:CCTGC:Cdonor_gain1.0000
10:48174953:CAC:Cacceptor_gain1.0000
10:48174955:CCTGG:Cacceptor_loss1.0000
10:48174956:C:CCacceptor_gain1.0000
10:48174956:CTGGG:Cacceptor_loss1.0000
10:48174957:T:Aacceptor_loss1.0000
10:48175844:AC:Adonor_gain1.0000
10:48175845:CC:Cdonor_gain1.0000
10:48175863:T:TAdonor_gain1.0000
10:48178045:A:ACdonor_gain1.0000
10:48178046:C:CCdonor_gain1.0000
10:48183363:C:CAdonor_gain1.0000
10:48183372:T:TAdonor_gain1.0000
10:48187186:CCATA:Cdonor_loss1.0000
10:48187187:CATA:Cdonor_loss1.0000
10:48187188:ATAC:Adonor_loss1.0000
10:48187189:TA:Tdonor_loss1.0000
10:48187190:A:Cdonor_loss1.0000
10:48187191:C:CAdonor_loss1.0000
10:48187288:AGGGG:Aacceptor_gain1.0000
10:48187289:GGGG:Gacceptor_gain1.0000
10:48187290:GGG:Gacceptor_gain1.0000
10:48187291:GG:Gacceptor_gain1.0000
10:48187291:GGCTG:Gacceptor_loss1.0000
10:48187293:C:CCacceptor_gain1.0000

AlphaMissense

8547 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:48171160:A:GF1091S0.996
10:48171159:G:CF1091L0.993
10:48171159:G:TF1091L0.993
10:48171161:A:GF1091L0.993
10:48171043:T:AD1130V0.990
10:48171043:T:GD1130A0.990
10:48171163:C:TG1090E0.990
10:48171037:A:GI1132T0.989
10:48171043:T:CD1130G0.989
10:48171037:A:TI1132N0.988
10:48171044:C:GD1130H0.988
10:48171032:C:GA1134P0.987
10:48171037:A:CI1132S0.987
10:48249078:G:CF84L0.987
10:48249078:G:TF84L0.987
10:48249080:A:GF84L0.987
10:48171073:G:TA1120D0.986
10:48171055:A:TI1126N0.984
10:48171100:A:GI1111T0.984
10:48184586:A:GL855S0.984
10:48171100:A:CI1111S0.983
10:48178057:A:GF962S0.983
10:48168650:A:GL1161P0.981
10:48171164:C:GG1090R0.981
10:48171164:C:TG1090R0.981
10:48171156:A:CS1092R0.979
10:48171156:A:TS1092R0.979
10:48171158:T:GS1092R0.979
10:48175854:A:GI994T0.978
10:48168650:A:TL1161H0.976

dbSNP variants (sampled 300 via entrez): RS1000010349 (10:48189409 G>A), RS1000021197 (10:48218438 C>A,G), RS1000053387 (10:48224847 G>A,T), RS1000076901 (10:48231494 T>G), RS1000159264 (10:48248179 C>G,T), RS1000172559 (10:48250175 C>A), RS1000179280 (10:48208776 C>T), RS1000209009 (10:48207440 T>C), RS1000299296 (10:48231057 C>T), RS1000317810 (10:48247863 A>G), RS1000320814 (10:48236949 T>C), RS1000348668 (10:48255918 A>C), RS1000401651 (10:48217602 T>C,G), RS1000419806 (10:48261984 T>A), RS1000420897 (10:48223280 A>C)

Disease associations

OMIM: gene MIM:613323 | 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
GCST003518_9Daytime sleep phenotypes4.000000e-06
GCST003997_7Myopia4.000000e-13
GCST006291_29Spherical equivalent or myopia (age of diagnosis)2.000000e-13
GCST010002_287Refractive error2.000000e-49

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007828daytime rest measurement
EFO:0004847age at onset

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
(+)-JQ1 compounddecreases expression2
Aflatoxin B1decreases methylation, increases methylation2
6,7-dimethoxy-2-(pyrrolidin-1-yl)-N-(5-(pyrrolidin-1-yl)pentyl)quinazolin-4-amineincreases expression1
OTX015decreases expression1
mivebresibdecreases expression1
methyleugenoldecreases expression1
sodium arsenitedecreases expression1
tebuconazoledecreases expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
Resveratroldecreases expression, affects cotreatment1
Acetaminophenincreases expression1
Arsenicaffects methylation1
Benzo(a)pyreneaffects methylation, increases methylation1
Calcitrioldecreases expression, affects cotreatment1
Copperaffects cotreatment, decreases expression1
Phthalic Acidsdecreases expression1
Rotenonedecreases expression1
Testosteronedecreases expression, affects cotreatment1
Tobacco Smoke Pollutiondecreases expression1
Urethanedecreases expression1
Okadaic Aciddecreases expression1
Permethrindecreases expression1
S-Nitrosoglutathioneincreases expression1

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.