MARCHF3

gene
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Also known as MGC48332MARCH-IIIRNF173

Summary

MARCHF3 (membrane associated ring-CH-type finger 3, HGNC:28728) is a protein-coding gene on chromosome 5q23.2, encoding E3 ubiquitin-protein ligase MARCHF3 (Q86UD3). E3 ubiquitin-protein ligase which may be involved in endosomal trafficking.

This gene encodes a member of the membrane-associated RING-CH (MARCH) family. The encoded protein is an E3 ubiquitin-protein ligase that may be involved in regulation of the endosomal transport pathway.

Source: NCBI Gene 115123 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 37 total
  • MANE Select transcript: NM_178450

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28728
Approved symbolMARCHF3
Namemembrane associated ring-CH-type finger 3
Location5q23.2
Locus typegene with protein product
StatusApproved
AliasesMGC48332, MARCH-III, RNF173
Ensembl geneENSG00000173926
Ensembl biotypeprotein_coding
OMIM613333
Entrez115123

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000308660, ENST00000502289, ENST00000504239, ENST00000506088, ENST00000515241, ENST00000892692, ENST00000892693, ENST00000892694, ENST00000928509, ENST00000928510, ENST00000928511, ENST00000968913

RefSeq mRNA: 1 — MANE Select: NM_178450 NM_178450

CCDS: CCDS4141

Canonical transcript exons

ENST00000308660 — 5 exons

ExonStartEnd
ENSE00001178483126878185126878394
ENSE00001178489126914930126915134
ENSE00001242174127030350127030558
ENSE00001242185126867714126870791
ENSE00003676575126917984126918227

Expression profiles

Bgee: expression breadth ubiquitous, 227 present calls, max score 91.95.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.5785 / max 337.6123, expressed in 1687 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
6320915.32461632
632100.9670567
632110.199356
632080.048910
632060.033914
632120.00492

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pancreatic ductal cellCL:000207991.95silver quality
spermCL:000001991.10gold quality
left testisUBERON:000453390.05gold quality
right testisUBERON:000453489.71gold quality
skin of legUBERON:000151189.13gold quality
heart left ventricleUBERON:000208488.61gold quality
testisUBERON:000047388.56gold quality
cardiac ventricleUBERON:000208288.32gold quality
skin of abdomenUBERON:000141688.31gold quality
male germ cellCL:000001588.00gold quality
apex of heartUBERON:000209887.58gold quality
adrenal tissueUBERON:001830387.22gold quality
right atrium auricular regionUBERON:000663187.21gold quality
zone of skinUBERON:000001487.08gold quality
mucosa of transverse colonUBERON:000499185.95gold quality
omental fat padUBERON:001041485.95gold quality
peritoneumUBERON:000235885.90gold quality
heartUBERON:000094885.85gold quality
rectumUBERON:000105285.83gold quality
adipose tissue of abdominal regionUBERON:000780885.34gold quality
gall bladderUBERON:000211085.29gold quality
heart right ventricleUBERON:000208085.14gold quality
cardiac atriumUBERON:000208185.10gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.83gold quality
mucosa of sigmoid colonUBERON:000499384.82gold quality
cortical plateUBERON:000534384.79gold quality
colonic mucosaUBERON:000031784.34gold quality
lower esophagus mucosaUBERON:003583484.05gold quality
epithelial cell of pancreasCL:000008383.46gold quality
medial globus pallidusUBERON:000247783.26gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-MTAB-10042yes24.58
E-GEOD-135922yes9.48
E-HCAD-25yes4.77
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

127 targeting MARCHF3, 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-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-3646100.0073.565283
HSA-MIR-126-5P100.0072.713180
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-223-3P99.9970.141140
HSA-MIR-453499.9966.581907
HSA-MIR-607799.9968.042299
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-1213699.9872.815713
HSA-MIR-1229-3P99.9766.49906
HSA-MIR-807599.9767.20962
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-96-5P99.9572.802140
HSA-MIR-144-3P99.9473.982698
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-1213399.9271.822006
HSA-MIR-568099.9169.833421
HSA-MIR-1271-5P99.9171.991972

Literature-anchored findings (GeneRIF, showing 3)

  • LPS activation of TLR4 significantly increased MARCH3 expression and that siRNA against MARCH3 prevented the decrease in FcgammaRIIb following LPS treatment. (PMID:26694610)
  • Report shows that silencing MARCH3 protects the endothelial barrier and upregulates OCLN in MARCH3-depleted cells. MARCH3 silencing results in the strengthening of cell-cell contacts and inactivates FoxO1. (PMID:27616439)
  • RNF173 suppresses RAF/MEK/ERK signaling to regulate invasion and metastasis via GRB2 ubiquitination in Hepatocellular Carcinoma. (PMID:37626338)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriozgc:158785ENSDARG00000062959
mus_musculusMarchf3ENSMUSG00000032656
rattus_norvegicusMarchf3ENSRNOG00000023013
caenorhabditis_elegansmarc-3WBGENE00007643

Paralogs (6): MARCHF2 (ENSG00000099785), MARCHF9 (ENSG00000139266), MARCHF4 (ENSG00000144583), MARCHF1 (ENSG00000145416), MARCHF8 (ENSG00000165406), MARCHF11 (ENSG00000183654)

Protein

Protein identifiers

E3 ubiquitin-protein ligase MARCHF3Q86UD3 (reviewed: Q86UD3)

Alternative names: Membrane-associated RING finger protein 3, Membrane-associated RING-CH protein III, RING finger protein 173, RING-type E3 ubiquitin transferase MARCHF3

All UniProt accessions (1): Q86UD3

UniProt curated annotations — full annotation on UniProt →

Function. E3 ubiquitin-protein ligase which may be involved in endosomal trafficking. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates.

Subunit / interactions. Interacts with MARCHF2 and STX6.

Subcellular location. Cytoplasmic vesicle membrane. Early endosome membrane.

Domain organisation. The RING-CH-type zinc finger domain is required for E3 ligase activity.

Pathway. Protein modification; protein ubiquitination.

Isoforms (2)

UniProt IDNamesCanonical?
Q86UD3-11yes
Q86UD3-22

RefSeq proteins (1): NP_848545* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001841Znf_RINGDomain
IPR011016Znf_RING-CHDomain
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily

Pfam: PF12906

UniProt features (17 total): binding site 8, transmembrane region 2, modified residue 2, splice variant 2, chain 1, sequence variant 1, zinc finger region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86UD3-F171.560.34

Functional residue map

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

Ligand- & substrate-binding residues (8): 113; 116; 71; 74; 87; 89; 97; 100

Post-translational modifications (2): 237, 243

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 186 (showing top): GSE45365_NK_CELL_VS_BCELL_DN, TAATAAT_MIR126, PEREZ_TP63_TARGETS, GOBP_VESICLE_MEDIATED_TRANSPORT, TAL1ALPHAE47_01, DOANE_BREAST_CANCER_CLASSES_DN, TGTGTGA_MIR377, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, ONDER_CDH1_TARGETS_2_UP, BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP, AACTTT_UNKNOWN, PEREZ_TP53_AND_TP63_TARGETS, LIU_CMYB_TARGETS_UP, GOBP_IMPORT_INTO_CELL, LIU_VMYB_TARGETS_UP

GO Biological Process (2): endocytosis (GO:0006897), protein ubiquitination (GO:0016567)

GO Molecular Function (6): ubiquitin-protein transferase activity (GO:0004842), zinc ion binding (GO:0008270), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (6): lysosome (GO:0005764), endosome (GO:0005768), early endosome membrane (GO:0031901), membrane (GO:0016020), cytoplasmic vesicle membrane (GO:0030659), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasmic vesicle2
vesicle budding from membrane1
membrane invagination1
vesicle-mediated transport1
import into cell1
protein modification by small protein conjugation1
ubiquitin-like protein transferase activity1
transition metal ion binding1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
binding1
catalytic activity1
cation binding1
lytic vacuole1
endomembrane system1
early endosome1
endosome membrane1
cellular anatomical structure1
vesicle membrane1
cytoplasm1
intracellular vesicle1

Protein interactions and networks

STRING

644 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MARCHF3STX6O43752907
MARCHF3TGOLN2O43493777
MARCHF3MARCHF10Q8NA82627
MARCHF3SPMIP10Q6ZNM6573
MARCHF3C5orf63A6NC05570
MARCHF3TFRCP02786563
MARCHF3MARCHF7Q9H992489
MARCHF3MINAR2P59773432
MARCHF3HSPB3Q12988428
MARCHF3GRAMD2BQ96HH9404
MARCHF3MARCHF5Q9NX47398
MARCHF3TMEM215Q68D42388
MARCHF3VAMP3Q15836367
MARCHF3LRP2BPQ9P2M1357
MARCHF3ISOC1Q96CN7350

IntAct

136 interactions, top by confidence:

ABTypeScore
DLG1MARCHF3psi-mi:“MI:0915”(physical association)0.610
MARCHF3DLG1psi-mi:“MI:0407”(direct interaction)0.610
MARCHF3APOL2psi-mi:“MI:0915”(physical association)0.560
MARCHF3FATE1psi-mi:“MI:0915”(physical association)0.560
UBE2KMARCHF3psi-mi:“MI:0915”(physical association)0.560
MARCHF3DLG2psi-mi:“MI:0407”(direct interaction)0.440
MARCHF3DLG4psi-mi:“MI:0407”(direct interaction)0.440
MARCHF3MAGI3psi-mi:“MI:0407”(direct interaction)0.440
MARCHF3DLG3psi-mi:“MI:0407”(direct interaction)0.440
MARCHF3SNTA1psi-mi:“MI:0407”(direct interaction)0.440
MARCHF3SNX27psi-mi:“MI:0407”(direct interaction)0.440
MARCHF3MAGI2psi-mi:“MI:0407”(direct interaction)0.440
MARCHF3LNX2psi-mi:“MI:0407”(direct interaction)0.440
MARCHF3SNTB1psi-mi:“MI:0407”(direct interaction)0.440
MARCHF3PDZD7psi-mi:“MI:0407”(direct interaction)0.440
MARCHF3PTPN3psi-mi:“MI:0407”(direct interaction)0.440
MARCHF3SYNJ2BPpsi-mi:“MI:0407”(direct interaction)0.440
MARCHF3MAST2psi-mi:“MI:0407”(direct interaction)0.440
MARCHF3MAGI1psi-mi:“MI:0407”(direct interaction)0.440
MARCHF3GORASP2psi-mi:“MI:0407”(direct interaction)0.440
MARCHF3SCRIBpsi-mi:“MI:0407”(direct interaction)0.440

BioGRID (55): MARCH3 (Two-hybrid), MARCH3 (Two-hybrid), BAG2 (Affinity Capture-MS), ILF3 (Affinity Capture-MS), TFRC (Affinity Capture-MS), TMEM201 (Affinity Capture-MS), RNFT1 (Affinity Capture-MS), NDUFS2 (Affinity Capture-MS), TNFRSF10B (Affinity Capture-MS), ITCH (Affinity Capture-MS), NOTCH2 (Affinity Capture-MS), NCSTN (Affinity Capture-MS), SLC3A2 (Affinity Capture-MS), ENDOD1 (Affinity Capture-MS), ATF6B (Affinity Capture-MS)

ESM2 similar proteins: A0A571BF63, A0JMQ9, A0JN69, A1L1R5, E7EZI4, O41933, P0C7U3, P33279, P40145, P97490, Q0IH10, Q0VD59, Q11122, Q1L8G6, Q1LVZ2, Q28EX7, Q28GL3, Q28IK8, Q32L65, Q3UF64, Q4R8E0, Q5I0I2, Q5M7Z0, Q5PQ35, Q5RAG4, Q5T0T0, Q5XH39, Q5XIE5, Q68FA7, Q6NRX0, Q6NTV1, Q6NZ21, Q6NZQ8, Q6ZPS6, Q6ZUJ8, Q803Q4, Q86UD3, Q8BGN6, Q8BPQ7, Q8BRX9

Diamond homologs: A0JN69, A6NNE9, A6P320, F4JKK0, O60103, O60337, P40318, P90489, P90495, Q0IH10, Q0P496, Q0VD59, Q1LVZ2, Q28EX7, Q32L65, Q3TZ87, Q5I0I2, Q5PQ35, Q5R9W1, Q5T0T0, Q5XIE5, Q5XIV2, Q68FA7, Q6NZQ8, Q6ZQ89, Q80TE3, Q86UD3, Q86YJ5, Q8BRX9, Q8CBH7, Q8TCQ1, Q99M02, Q9DBD2, Q9P0N8, Q9P2E8, Q0X0A5, Q28IK8, Q3KNM2, Q3ZC24, Q5R9W2

SIGNOR signaling

1 interactions.

AEffectBMechanism
Ub:E2“up-regulates activity”MARCHF3ubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 87 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
Assembly and cell surface presentation of NMDA receptors836.2×4e-09
Neurexins and neuroligins1035.2×3e-11
Protein-protein interactions at synapses628.5×4e-06
Antigen processing: Ubiquitination & Proteasome degradation96.0×3e-04

GO biological processes:

GO termPartnersFoldFDR
establishment or maintenance of epithelial cell apical/basal polarity963.0×5e-12
protein localization to synapse655.4×2e-07
receptor clustering645.1×4e-07
regulation of postsynaptic membrane neurotransmitter receptor levels635.8×2e-06
protein-containing complex assembly912.3×3e-06
protein K48-linked ubiquitination612.2×5e-04
cell-cell adhesion89.8×1e-04
chemical synaptic transmission76.5×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance31
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1651 predictions. Top by Δscore:

VariantEffectΔscore
5:126917983:CCT:Cdonor_gain1.0000
5:126918006:C:CTdonor_gain1.0000
5:126918006:CTA:Cdonor_gain1.0000
5:126918007:T:TTdonor_gain1.0000
5:126918054:A:ACdonor_gain1.0000
5:126918055:C:CCdonor_gain1.0000
5:126878183:A:ACdonor_gain0.9900
5:126878184:C:CCdonor_gain0.9900
5:126878390:AGCCA:Aacceptor_gain0.9900
5:126878399:CAGG:Cacceptor_gain0.9900
5:126913301:T:TAdonor_gain0.9900
5:126914924:A:ACdonor_gain0.9900
5:126914925:C:CCdonor_gain0.9900
5:126917978:TACTA:Tdonor_loss0.9900
5:126917979:ACTAC:Adonor_loss0.9900
5:126917981:TAC:Tdonor_loss0.9900
5:126917982:ACCTC:Adonor_loss0.9900
5:126917983:C:CAdonor_loss0.9900
5:126918008:A:ACdonor_gain0.9900
5:126918009:C:CCdonor_gain0.9900
5:126918029:T:TAdonor_gain0.9900
5:126918045:G:Adonor_gain0.9900
5:126918224:CCAT:Cacceptor_gain0.9900
5:126918225:CAT:Cacceptor_gain0.9900
5:126918225:CATC:Cacceptor_gain0.9900
5:126918228:C:CCacceptor_gain0.9900
5:126870791:CCT:Cacceptor_loss0.9800
5:126870792:CTG:Cacceptor_loss0.9800
5:126878184:CTA:Cdonor_gain0.9800
5:126878391:GCCA:Gacceptor_gain0.9800

AlphaMissense

1632 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:126870753:C:AW214C1.000
5:126870753:C:GW214C1.000
5:126870755:A:GW214R1.000
5:126870755:A:TW214R1.000
5:126878193:A:GW199R1.000
5:126878193:A:TW199R1.000
5:126878225:A:GL188P1.000
5:126878225:A:TL188H1.000
5:126878234:A:GL185P1.000
5:126878292:A:GC166R1.000
5:126878294:A:GL165P1.000
5:126878300:C:TG163D1.000
5:126878312:G:TA159D1.000
5:126878318:G:CP157R1.000
5:126878324:A:TI155K1.000
5:126878345:T:GD148A1.000
5:126914964:A:GF120S1.000
5:126914975:G:CC116W1.000
5:126914976:C:AC116F1.000
5:126914976:C:GC116S1.000
5:126914976:C:TC116Y1.000
5:126914977:A:GC116R1.000
5:126914977:A:TC116S1.000
5:126914984:A:CC113W1.000
5:126914985:C:AC113F1.000
5:126914985:C:GC113S1.000
5:126914985:C:TC113Y1.000
5:126914986:A:GC113R1.000
5:126914986:A:TC113S1.000
5:126915009:A:GL105P1.000

dbSNP variants (sampled 300 via entrez): RS1000016749 (5:126887998 A>C,G), RS1000040125 (5:126894362 G>A,C), RS1000067227 (5:126937359 C>A,T), RS1000070993 (5:126980880 G>T), RS1000109485 (5:127000113 A>G), RS1000122980 (5:126917907 T>G), RS1000128944 (5:126926946 T>A), RS1000172122 (5:126928060 A>G), RS1000209011 (5:126872057 G>A), RS1000215133 (5:126869798 C>T), RS1000246442 (5:127013460 T>C), RS1000296600 (5:126880970 T>C), RS1000302519 (5:126881599 T>G), RS1000327086 (5:126899955 A>G), RS1000337602 (5:126874723 T>A,C,G)

Disease associations

OMIM: gene MIM:613333 | 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
GCST008534_1Hearing loss in Charcot-Marie-Tooth disease 1A2.000000e-07
GCST009240_392Serum metabolite levels (CMS)4.000000e-10
GCST009242_200Serum metabolite levels2.000000e-06
GCST009462_62Optic disc size1.000000e-08
GCST009531_6Body fat percentage9.000000e-08
GCST010436_4Type 2 diabetes1.000000e-07
GCST90002387_307Immature fraction of reticulocytes2.000000e-10

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007800body fat percentage

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
(+)-JQ1 compoundincreases expression4
Valproic Acidincreases expression3
entinostatincreases expression, affects cotreatment2
Benzo(a)pyreneincreases methylation, increases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Silicon Dioxideincreases expression2
aristolochic acid Iincreases expression1
GSK-J4increases expression1
aminomethylphosphonic acid (AMPA)decreases expression1
propionaldehydeincreases expression1
bisphenol Adecreases expression1
sodium arseniteaffects methylation1
cobaltous chloridedecreases expression1
butyraldehydeincreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
hydroquinoneincreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
2-palmitoylglycerolincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression, decreases expression1
abrineincreases expression1
Grape Seed Proanthocyanidinsaffects cotreatment, increases expression1
dorsomorphinincreases expression, decreases expression, affects cotreatment1
Dasatinibdecreases expression1
Zoledronic Acidincreases expression1
Arsenic Trioxidedecreases expression1
Acetaminophenincreases expression1
Calcitriolincreases expression1
Catechinaffects cotreatment, increases expression1
Cytarabinedecreases expression1
Lipopolysaccharidesincreases 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.