MACF1

gene
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Also known as KIAA0465ACF7ABP620KIAA1251MACFFLJ45612FLJ46776Lnc-PMIF

Summary

MACF1 (microtubule actin crosslinking factor 1, HGNC:13664) is a protein-coding gene on chromosome 1p34.3, encoding Microtubule-actin cross-linking factor 1, isoforms 6/7 (O94854).

This gene encodes a large protein containing numerous spectrin and leucine-rich repeat (LRR) domains. The encoded protein is a member of a family of proteins that form bridges between different cytoskeletal elements. This protein facilitates actin-microtubule interactions at the cell periphery and couples the microtubule network to cellular junctions. Alternative splicing results in multiple transcript variants, but the full-length nature of some of these variants has not been determined.

Source: NCBI Gene 23499 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): lissencephaly 9 with complex brainstem malformation (Strong, GenCC) — +2 more curated relationships
  • GWAS associations: 39
  • Clinical variants (ClinVar): 1,957 total — 4 pathogenic, 12 likely-pathogenic
  • Phenotypes (HPO): 49
  • MANE Select transcript: NM_001394062

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13664
Approved symbolMACF1
Namemicrotubule actin crosslinking factor 1
Location1p34.3
Locus typegene with protein product
StatusApproved
AliasesKIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776, Lnc-PMIF
Ensembl geneENSG00000127603
Ensembl biotypeprotein_coding
OMIM608271
Entrez23499

Gene structure

Transcript identifiers

Ensembl transcripts: 58 — 24 retained_intron, 20 protein_coding, 10 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay

ENST00000289893, ENST00000360115, ENST00000361689, ENST00000372915, ENST00000372925, ENST00000422234, ENST00000442046, ENST00000446276, ENST00000462103, ENST00000462496, ENST00000467673, ENST00000469366, ENST00000469490, ENST00000472385, ENST00000473843, ENST00000476350, ENST00000480624, ENST00000484393, ENST00000484793, ENST00000485063, ENST00000494012, ENST00000496360, ENST00000496804, ENST00000497807, ENST00000497964, ENST00000524432, ENST00000528611, ENST00000530262, ENST00000530275, ENST00000564288, ENST00000567887, ENST00000602421, ENST00000602528, ENST00000671089, ENST00000672812, ENST00000673706, ENST00000673926, ENST00000673980, ENST00000683517, ENST00000686067, ENST00000686260, ENST00000686657, ENST00000686687, ENST00000686941, ENST00000687271, ENST00000687885, ENST00000687997, ENST00000688212, ENST00000688426, ENST00000688822, ENST00000689726, ENST00000689911, ENST00000690080, ENST00000690939, ENST00000691623, ENST00000693209, ENST00000693392, ENST00000693546

RefSeq mRNA: 3 — MANE Select: NM_001394062 NM_001394062, NM_001397473, NM_012090

CCDS: CCDS435, CCDS90919

Canonical transcript exons

ENST00000564288 — 101 exons

ExonStartEnd
ENSE000010414073943777739438008
ENSE000010794753934080439340953
ENSE000010794823934050239340717
ENSE000010794853934697739347210
ENSE000010794983933718239337331
ENSE000012172373929762039297745
ENSE000012181343930021039300362
ENSE000014589393946954739469615
ENSE000015948163944271439442911
ENSE000015956263944769239447898
ENSE000015992473943555839435761
ENSE000015998393938718739388658
ENSE000016125393937846139378523
ENSE000016154463943253539432654
ENSE000016217223929276639292843
ENSE000016233663945837039458490
ENSE000016323093943441439434632
ENSE000016330583928318939283301
ENSE000016337553945908639459249
ENSE000016419563928560439285758
ENSE000016431683938024439380373
ENSE000016510403944241239442567
ENSE000016511283945105239451211
ENSE000016519723943070239430908
ENSE000016546623929191039292038
ENSE000016694553944214739442320
ENSE000016731403944743239447587
ENSE000016792083929578739295882
ENSE000016915193928406639284185
ENSE000016933023937247939372596
ENSE000017128683943304839433155
ENSE000017131643928529739285390
ENSE000017222363945215639452350
ENSE000017271623938195339382152
ENSE000017276663944859439448763
ENSE000017343323938543439385929
ENSE000017363923942924239429326
ENSE000017385343944466239444835
ENSE000017419893948460139484730
ENSE000017436473945490939455097
ENSE000017514653944344639443574
ENSE000017550693942982739430068
ENSE000017562853942745539427614
ENSE000017609273928728639287562
ENSE000017614063942796139428287
ENSE000017653603929504639295150
ENSE000017693283942273039422900
ENSE000017716173929345839293619
ENSE000017740483944803339448152
ENSE000017796693942402839424194
ENSE000017801663945268439452812
ENSE000017842673942237439422535
ENSE000017888843945370739453850
ENSE000017936523946509539465112
ENSE000018050453937920339379444
ENSE000018961383920469539205131
ENSE000021566303933120339336653
ENSE000022732893928220839282374
ENSE000026075063925184639251941
ENSE000027088653928433339284428
ENSE000034618013928508339285210
ENSE000034620033936814839368314
ENSE000034666633925001439250103
ENSE000034740743931024539310428
ENSE000034842273930957039309696
ENSE000034921203946063239460794
ENSE000034997253931966439319747
ENSE000034998853931551339315691
ENSE000035186833944122439441325
ENSE000035200923931639139316529
ENSE000035266873936079339361001
ENSE000035271873935300739353231
ENSE000035317533944195239442053
ENSE000035357133936136039361677
ENSE000035377453943927439439500
ENSE000035463813947979839480009
ENSE000035685043946188339462037
ENSE000035847863923118239231243
ENSE000035917343931083139311000
ENSE000036017793946361239463686
ENSE000036027693925793639258028
ENSE000036053153932721839327353
ENSE000036155183937003039370186
ENSE000036167513944100339441125
ENSE000036210223935914139359264
ENSE000036251533948092039481030
ENSE000036391433928340939283515
ENSE000036494503931721439317407
ENSE000036498983932464639324734
ENSE000036709953946861539468732
ENSE000036743523931845339318615
ENSE000036747543935737539357893
ENSE000036780723935869739358873
ENSE000036796033932260839322715
ENSE000036830453935078539351018
ENSE000036844633932419339324345
ENSE000036888283934947839349627
ENSE000036904653930292439303078
ENSE000037840463932291039323008
ENSE000037906873925429839254375
ENSE000039266423948553839487138

Expression profiles

Bgee: expression breadth ubiquitous, 303 present calls, max score 99.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 53.9487 / max 645.2489, expressed in 1820 samples.

FANTOM5 promoters (31 alternative TSS)

Promoter IDTPM avgSamples expressed
226920.42581772
231210.31621519
22906.1927461
23113.95401365
22953.3227590
22813.27261051
22752.9799459
22802.80161034
22792.6197855
22892.4391423

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
inferior olivary complexUBERON:000212799.37gold quality
dorsal motor nucleus of vagus nerveUBERON:000287099.36gold quality
right lungUBERON:000216799.32gold quality
calcaneal tendonUBERON:000370199.29gold quality
colonic epitheliumUBERON:000039799.25gold quality
corpus callosumUBERON:000233699.18gold quality
middle temporal gyrusUBERON:000277199.03gold quality
saphenous veinUBERON:000731899.02gold quality
upper lobe of left lungUBERON:000895298.99gold quality
ventricular zoneUBERON:000305398.95gold quality
upper lobe of lungUBERON:000894898.93gold quality
right coronary arteryUBERON:000162598.89gold quality
lateral globus pallidusUBERON:000247698.86gold quality
body of uterusUBERON:000985398.84gold quality
skin of legUBERON:000151198.83gold quality
lungUBERON:000204898.78gold quality
myometriumUBERON:000129698.75gold quality
skin of abdomenUBERON:000141698.74gold quality
cortical plateUBERON:000534398.74gold quality
lower esophagus muscularis layerUBERON:003583398.69gold quality
lower esophagusUBERON:001347398.68gold quality
visceral pleuraUBERON:000240198.65gold quality
popliteal arteryUBERON:000225098.63gold quality
tibial arteryUBERON:000761098.63gold quality
muscle layer of sigmoid colonUBERON:003580598.62gold quality
skin of hipUBERON:000155498.61gold quality
arteryUBERON:000163798.61gold quality
left uterine tubeUBERON:000130398.60gold quality
endothelial cellCL:000011598.59gold quality
aortaUBERON:000094798.59gold quality

Single-cell (SCXA)

Detected in 15 experiment(s), a significant marker in 10.

ExperimentMarker?Max mean expression
E-ANND-2yes4485.36
E-HCAD-35yes3742.45
E-CURD-126yes2233.54
E-GEOD-135922yes33.13
E-CURD-122yes24.03
E-HCAD-25yes21.34
E-CURD-112yes20.27
E-GEOD-84465yes10.81
E-GEOD-137537yes5.36
E-GEOD-150728no2297.54
E-HCAD-6no716.49
E-CURD-55no577.08
E-MTAB-7606no413.95
E-CURD-97no279.24
E-ANND-3no0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 28)

  • p230, through its interaction with MACF1, provides the molecular link for transport of GPI-anchored proteins along the microtubule and actin cytoskeleton from the TGN to the cell periphery. (PMID:15265687)
  • In two lung cell lines, MACF1b was chiefly localized to the Golgi complex. The domain of MACF1b that targets it to the Golgi was found at the N-terminal part of the region that contains the plakin repeats. (PMID:16076900)
  • This protein has been found differentially expressed in the Wernicke’s Area from patients with schizophrenia. (PMID:19405953)
  • ACF7 targeting to the plasma membrane is both required and sufficient for microtubule capture downstream of ErbB2. (PMID:20937854)
  • uncovered a role for ELMO in the recruitment of ACF7 to the membrane to promote microtubule capture and stability (PMID:23184944)
  • Duplication in the microtubule-actin cross-linking factor 1 gene causes neuromuscular diseases. (PMID:24899269)
  • MACF1b may contribute to the genetic etiology and mechanistic causation of Parkinson’s disease. (PMID:27021023)
  • ACF7, a member of the spectraplakin family of cytoskeletal crosslinking proteins, interacts with Nezha (also called CAMSAP3) at the minus ends of noncentrosomal microtubules and anchors them to actin filaments. (PMID:27693509)
  • in mammalian intestinal epithelial cells, the spectraplakin ACF7 (also known as MACF1) specifically binds to CAMSAP3 and is required for the apical localization of CAMSAP3-decorated microtubule minus ends. (PMID:27802168)
  • the present study represents the first investigation on the functional role of MACF1 in tumor cell biology, as well as demonstrates its potential as a unique biomarker that can be targeted synergistically with TMZ as part of a combinatorial therapeutic approach for the treatment of genetically multifarious glioblastomas (PMID:27959385)
  • Loss of ACF7 leads to aberrant microtubule organization, tight junction stabilization and impaired wound closure in vitro. ACF7 level is also correlated with development and progression of ulcerative colitis (UC) in patients. (PMID:28541346)
  • Study summarized the physiological role of MACF1 as well as its pathological one in various cancers. MACF1 comprises different isoforms, and is broadly expressed in brain, spinal cord, lung, kidney, heart, bone and skeletal muscles tissues. It plays a crucial role in cell proliferation, migration and cell signaling, and is also closely associated with many cancer. (PMID:28782898)
  • MACF1 overexpression triggered a drastic increase in osteogenic gene expression, alkaline phosphatase activity, and matrix mineralization in vitro. Mouse calvarial thickness, mineral apposition rate, and osteogenic marker protein expression were significantly enhanced by local transfection. In addition, MACF1 overexpression promoted beta-catenin expression and signaling. (PMID:29334773)
  • Three de novo variants in MACF1 have been observed in large schizophrenia cohorts. (PMID:30471716)
  • In this study, uncontrolled Diabetes mellitus (DM) had a remote impact on different components of the platelet transcriptome. Increased expression of MACF1, together with supporting predicted mRNA-miRNA interactions as well as reduced expression of RNYs in platelets, may reflect subclinical platelet activation in uncontrolled DM. (PMID:30519591)
  • Missense mutation in the MACF1 gene is associated with congenital myasthenia. (PMID:30842214)
  • MACF1 might lose the control of the whole cytoskeleton system, synapse might change and Alzheimer’s disease might develop (PMID:31383338)
  • Mesenchymal MACF1 Facilitates SMAD7 Nuclear Translocation to Drive Bone Formation. (PMID:32143362)
  • New insights into the genetic basis of premature ovarian insufficiency: Novel causative variants and candidate genes revealed by genomic sequencing. (PMID:33036707)
  • Lissencephaly with Brainstem Hypoplasia and Dysplasia: Think MACF1. (PMID:33511591)
  • Expression and Clinical Significance of Microtubule-Actin Cross-Linking Factor 1 in Serous Ovarian Cancer. (PMID:33573562)
  • Deubiquitylation and stabilization of Acf7 by ubiquitin carboxylterminal hydrolase 14 (USP14) is critical for NSCLC migration. (PMID:33737492)
  • The role of MACF1 on acute myeloid leukemia cell proliferation is involved in Runx2-targeted PI3K/Akt signaling. (PMID:35857251)
  • THADA, SDHAF4, and MACF1 Gene Polymorphisms and Placental Expression in Women with Gestational Diabetes. (PMID:36672824)
  • Role of microtubule actin crosslinking factor 1 (MACF1) in bipolar disorder pathophysiology and potential in lithium therapeutic mechanism. (PMID:37353479)
  • CircMACF1 alleviates myocardial fibrosis after acute myocardial infarction by suppressing cardiac fibroblast activation via the miR-16-5p/SMAD7 axis. (PMID:37713818)
  • LRRC1 knockdown downregulates MACF1 to inhibit the malignant progression of acute myeloid leukemia by inactivating beta-catenin/c-Myc signaling. (PMID:38165568)
  • Exosomal circMACF1 drives PI3K/AKT/mTOR-mediated autophagy suppression in laryngeal squamous cell carcinoma. (PMID:38372097)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusMacf1ENSMUSG00000028649
rattus_norvegicusMacf1ENSRNOG00000016047

Paralogs (36): SYNE2 (ENSG00000054654), SPTB (ENSG00000070182), ACTN1 (ENSG00000072110), ACTN2 (ENSG00000077522), DSP (ENSG00000096696), DRP2 (ENSG00000102385), SPTBN1 (ENSG00000115306), FLNC (ENSG00000128591), ACTN4 (ENSG00000130402), SYNE1 (ENSG00000131018), MICAL2 (ENSG00000133816), DTNA (ENSG00000134769), MICAL1 (ENSG00000135596), FLNB (ENSG00000136068), SPTBN5 (ENSG00000137877), DTNB (ENSG00000138101), GAS2L3 (ENSG00000139354), DST (ENSG00000151914), UTRN (ENSG00000152818), SPTBN4 (ENSG00000160460), SPTA1 (ENSG00000163554), CLMN (ENSG00000165959), PKHD1 (ENSG00000170927), SPTBN2 (ENSG00000173898), SYNE3 (ENSG00000176438), PLEC (ENSG00000178209), SMTNL2 (ENSG00000188176), FLNA (ENSG00000196924), SPTAN1 (ENSG00000197694), DMD (ENSG00000198947), PKHD1L1 (ENSG00000205038), DYTN (ENSG00000232125), MICAL3 (ENSG00000243156), ACTN3 (ENSG00000248746), EPPK1 (ENSG00000261150), GAS2L2 (ENSG00000270765)

Protein

Protein identifiers

Microtubule-actin cross-linking factor 1, isoforms 6/7O94854 (reviewed: O94854, Q9UPN3)

Alternative names: Uncharacterized protein KIAA0754

All UniProt accessions (23): Q9UPN3, A0A0A6YYJ5, A0A590UJG2, A0A5F9ZGX0, A0A669KB06, A0A669KB76, A0A669KB84, A0A669KBB0, A0A7P0MQR8, A0A804HL78, A0A8I5KY71, B4DQX9, E9PLY0, E9PLY5, E9PNZ4, E9PS75, H0Y314, H0Y390, H0Y4F5, H0Y6T5, H0Y7I1, H3BPE1, H3BQK9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm. Cytoskeleton.

Isoforms (7)

UniProt IDNamesCanonical?
O94854-36yes
O94854-47
Q9UPN3-11, Macf1b
Q9UPN3-22, Macf1a
Q9UPN3-33
Q9UPN3-45
Q9UPN3-54

RefSeq proteins (3): NP_001380991, NP_001384402, NP_036222 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002017Spectrin_repeatRepeat
IPR002048EF_hand_domDomain
IPR003108GAR_domDomain
IPR011992EF-hand-dom_pairHomologous_superfamily
IPR018159Spectrin/alpha-actininRepeat
IPR018247EF_Hand_1_Ca_BSBinding_site
IPR036534GAR_dom_sfHomologous_superfamily
IPR037727MCAF1-likeFamily
IPR001101Plectin_repeatRepeat
IPR001452SH3_domainDomain
IPR001589Actinin_actin-bd_CSConserved_site
IPR001715CH_domDomain
IPR035915Plakin_repeat_sfHomologous_superfamily
IPR036872CH_dom_sfHomologous_superfamily
IPR041573Desmoplakin_Spectrin-likeDomain
IPR041615Desmoplakin_SH3Domain
IPR043197PlakinFamily
IPR049538PCN-like_spectrin-like_rptRepeat

Pfam: PF00307, PF00435, PF00681, PF02187, PF13499, PF17902, PF18373, PF21019, PF21020, PF21097

UniProt features (243 total): repeat 65, modified residue 29, helix 25, compositionally biased region 21, region of interest 20, binding site 20, sequence variant 17, sequence conflict 12, strand 11, domain 9, splice variant 8, turn 4, chain 2

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
5X57X-RAY DIFFRACTION1.45
4Z6GX-RAY DIFFRACTION2.65
5VE9X-RAY DIFFRACTION2.79

Predicted structure (AlphaFold)

No AlphaFold model available for O94854 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

No AlphaFold model available for Q9UPN3 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Functional residue map

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

O94854 (canonical)

Ligand- & substrate-binding residues (10): 3181; 3183; 3185; 3187; 3192; 3217; 3219; 3221; 3223; 3228

Q9UPN3

Ligand- & substrate-binding residues (10): 7054; 7056; 7058; 7060; 7065; 7090; 7092; 7094; 7096; 7101

Post-translational modifications (29): 2077, 3122, 3331, 3927, 4495, 4496, 4521, 4836, 4962, 5435, 5808, 6032, 6210, 6967, 7254, 7279, 7292, 7330, 7333, 4 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 445 (showing top): FXR_IR1_Q6, GCM_MAP4K4, GOBP_INTERMEDIATE_FILAMENT_BASED_PROCESS, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, GOBP_NEURON_PROJECTION_EXTENSION, GOBP_REGULATION_OF_DEVELOPMENTAL_GROWTH, GOZGIT_ESR1_TARGETS_DN, GOBP_FOCAL_ADHESION_ASSEMBLY, GEORGES_CELL_CYCLE_MIR192_TARGETS, GOBP_REGULATION_OF_EPITHELIAL_CELL_MIGRATION, GOBP_GROWTH, MITSIADES_RESPONSE_TO_APLIDIN_DN, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY

GO Biological Process (15): regulation of epithelial cell migration (GO:0010632), Wnt signaling pathway (GO:0016055), positive regulation of Wnt signaling pathway (GO:0030177), regulation of cell migration (GO:0030334), regulation of microtubule-based process (GO:0032886), wound healing (GO:0042060), Golgi to plasma membrane protein transport (GO:0043001), intermediate filament cytoskeleton organization (GO:0045104), positive regulation of axon extension (GO:0045773), regulation of focal adhesion assembly (GO:0051893), regulation of neuron projection arborization (GO:0150011), regulation of anatomical structure morphogenesis (GO:0022603), regulation of cell projection organization (GO:0031344), regulation of multicellular organismal process (GO:0051239), establishment of protein localization to membrane (GO:0090150)

GO Molecular Function (10): calcium ion binding (GO:0005509), microtubule binding (GO:0008017), RNA binding (GO:0003723), actin binding (GO:0003779), structural molecule activity (GO:0005198), cadherin binding (GO:0045296), microtubule minus-end binding (GO:0051011), actin filament binding (GO:0051015), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (14): cytoskeleton (GO:0005856), cytoplasm (GO:0005737), Golgi apparatus (GO:0005794), microtubule (GO:0005874), plasma membrane (GO:0005886), actin cytoskeleton (GO:0015629), membrane (GO:0016020), ruffle membrane (GO:0032587), intermediate filament (GO:0005882), cell junction (GO:0030054), cell leading edge (GO:0031252), ciliary basal body (GO:0036064), cell projection (GO:0042995), organelle (GO:0043226)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure6
polymeric cytoskeletal fiber2
epithelial cell migration1
regulation of cell migration1
regulation of multicellular organismal process1
cell surface receptor signaling pathway1
positive regulation of signal transduction1
Wnt signaling pathway1
regulation of Wnt signaling pathway1
cell migration1
regulation of cell motility1
microtubule-based process1
regulation of cellular process1
response to wounding1
tissue regeneration1
Golgi to plasma membrane transport1
protein transport1
establishment of protein localization to plasma membrane1
protein localization to plasma membrane1
cytoskeleton organization1
intermediate filament-based process1
positive regulation of cell growth1
regulation of axon extension1
positive regulation of developmental growth1
axon extension1
positive regulation of axonogenesis1
regulation of cell-matrix adhesion1
focal adhesion assembly1
regulation of cell-substrate junction assembly1
regulation of cell morphogenesis1
regulation of cell projection organization1
neuron projection arborization1
anatomical structure morphogenesis1
regulation of developmental process1
cell projection organization1
regulation of cellular component organization1
multicellular organismal process1
regulation of biological process1
establishment of protein localization1
localization within membrane1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

31 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
YWHAZBLTP3Bpsi-mi:“MI:0914”(association)0.530
NRASESYT2psi-mi:“MI:2364”(proximity)0.480
MACF1RPL14psi-mi:“MI:0915”(physical association)0.400
CEP170P1PCYT1Apsi-mi:“MI:0914”(association)0.350
ImmtGOSR1psi-mi:“MI:0914”(association)0.350
APOA1CNMDpsi-mi:“MI:0914”(association)0.350
TNFRSF10Apsi-mi:“MI:0914”(association)0.350
HCN1POTEFpsi-mi:“MI:0914”(association)0.350
CLASP1KIF2Apsi-mi:“MI:0914”(association)0.350
CSNK2A1RPS3Apsi-mi:“MI:0914”(association)0.350
MAPRE1SCAMP1psi-mi:“MI:0914”(association)0.350
RBM14TBKBP1psi-mi:“MI:0914”(association)0.350
SNRPBDDX39Apsi-mi:“MI:0914”(association)0.350
SNRPCDDX39Apsi-mi:“MI:0914”(association)0.350
YWHABBRAFpsi-mi:“MI:0914”(association)0.350
YWHAEDEPDC5psi-mi:“MI:0914”(association)0.350
KRASESYT2psi-mi:“MI:2364”(proximity)0.270
HRASESYT2psi-mi:“MI:2364”(proximity)0.270
AGGF1BLTP3Bpsi-mi:“MI:2364”(proximity)0.270
BUD13RPSA2psi-mi:“MI:2364”(proximity)0.270
DGCR8VWA8psi-mi:“MI:2364”(proximity)0.270
RBM15ILVBLpsi-mi:“MI:2364”(proximity)0.270
RPS11ESYT2psi-mi:“MI:2364”(proximity)0.270
RPS3ESYT2psi-mi:“MI:2364”(proximity)0.270
SF3B4MED19psi-mi:“MI:2364”(proximity)0.270
UTP3NACApsi-mi:“MI:2364”(proximity)0.270
ZRANB2SBNO1psi-mi:“MI:2364”(proximity)0.270
EIF3GSBNO1psi-mi:“MI:2364”(proximity)0.270

BioGRID (44): KIAA0754 (Affinity Capture-RNA), KIAA0754 (Affinity Capture-RNA), KIAA0754 (Affinity Capture-RNA), KIAA0754 (Affinity Capture-MS), KIAA0754 (Affinity Capture-MS), KIAA0754 (Affinity Capture-RNA), KIAA0754 (Proximity Label-MS), KIAA0754 (Proximity Label-MS), KIAA0754 (Affinity Capture-MS), RPL14 (Proximity Label-MS), KIAA0754 (Proximity Label-MS), KIAA0754 (Affinity Capture-MS), KIAA0754 (Proximity Label-MS), KIAA0754 (Proximity Label-MS), KIAA0754 (Proximity Label-MS)

ESM2 similar proteins: A0A1B0GUW6, A1EGX6, A4FU49, A6NJ88, A6QP92, E9PAV3, E9Q0C6, F1QU13, O94854, P18583, P24587, P27546, P27816, P36225, P43597, P70670, Q08DY0, Q2T9N0, Q32L62, Q4R729, Q4V7A4, Q5H9T9, Q5M7W5, Q5SWP3, Q5XHX6, Q5XPK0, Q659K0, Q68DN1, Q68FX6, Q69ZZ9, Q6AZ54, Q6P6B1, Q6ZRG5, Q70KF4, Q710D7, Q810T2, Q8K4E0, Q8N3K9, Q8TCU4, Q8WWL7

Diamond homologs: A0A1L8H8C0, A0A1L8HFX9, D3ZHV2, D3ZUE1, O43903, O94854, P11862, Q03001, Q3UWW6, Q5SSG4, Q69ZZ9, Q86XJ1, Q8JZP9, Q8NHY3, Q91ZU6, Q99501, Q9QXZ0, Q9UPN3, Q9W3Y4, A0A8M2BID5, A5D7D1, D3ZEN0, D3ZHA0, D3ZQL6, E9Q557, F1LMV6, F1QH17, G3MWR8, G3V7L1, L7UZ85, M9MRD1, O13728, O15020, O43707, O75369, O76329, O88990, O97592, P05094, P05095

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 48 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
RAF activation545.4×3e-06
Signaling by high-kinase activity BRAF mutants542.9×4e-06
MAP2K and MAPK activation538.6×6e-06
Signaling by RAF1 mutants537.6×6e-06
Negative regulation of MAPK pathway535.9×6e-06
Signaling by moderate kinase activity BRAF mutants534.3×6e-06
Paradoxical activation of RAF signaling by kinase inactive BRAF534.3×6e-06
Signaling downstream of RAS mutants534.3×6e-06

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation521.0×1e-03
MAPK cascade517.4×1e-03
mRNA splicing, via spliceosome612.5×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

1957 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic4
Likely pathogenic12
Uncertain significance890
Likely benign603
Benign200

Top pathogenic / likely-pathogenic (16)

Variant IDHGVSClassification
1068756NM_001394062.1(MACF1):c.21878A>T (p.Asp7293Val)Pathogenic
1685933NM_001394062.1(MACF1):c.12265C>T (p.Gln4089Ter)Pathogenic
3767317NM_001394062.1(MACF1):c.8892del (p.Gln2964fs)Pathogenic
586948NM_001394062.1(MACF1):c.21707G>T (p.Cys7236Phe)Pathogenic
1676542NM_001394062.1(MACF1):c.1957C>T (p.Leu653Phe)Likely pathogenic
1694447NM_001394062.1(MACF1):c.21717G>T (p.Arg7239Ser)Likely pathogenic
1699453NM_001394062.1(MACF1):c.21803G>A (p.Arg7268His)Likely pathogenic
2431958NM_001394062.1(MACF1):c.7129dup (p.Arg2377fs)Likely pathogenic
2441775NM_001394062.1(MACF1):c.21820G>A (p.Val7274Met)Likely pathogenic
2499569NM_001394062.1(MACF1):c.21752G>C (p.Arg7251Pro)Likely pathogenic
3024134NM_001394062.1(MACF1):c.21679-2A>GLikely pathogenic
3065758NM_001394062.1(MACF1):c.16804-2A>GLikely pathogenic
3898866NM_001394062.1(MACF1):c.21443T>C (p.Met7148Thr)Likely pathogenic
4291812NM_001394062.1(MACF1):c.16149+1G>TLikely pathogenic
4813443NM_001394062.1(MACF1):c.20288T>G (p.Phe6763Cys)Likely pathogenic
599523NM_001394062.1(MACF1):c.22433G>A (p.Arg7478His)Likely pathogenic

SpliceAI

14189 predictions. Top by Δscore:

VariantEffectΔscore
1:39084435:GCTG:Gdonor_gain1.0000
1:39084439:G:GGdonor_gain1.0000
1:39231176:TTACA:Tacceptor_loss1.0000
1:39231179:CA:Cacceptor_loss1.0000
1:39231180:A:AGacceptor_gain1.0000
1:39231180:A:Gacceptor_loss1.0000
1:39231181:G:GAacceptor_gain1.0000
1:39231181:GAT:Gacceptor_gain1.0000
1:39231242:AGG:Adonor_loss1.0000
1:39231244:GTA:Gdonor_loss1.0000
1:39231245:T:Adonor_loss1.0000
1:39250006:A:AGacceptor_gain1.0000
1:39250007:T:Gacceptor_gain1.0000
1:39250100:ACTGG:Adonor_loss1.0000
1:39250102:TGG:Tdonor_loss1.0000
1:39250104:G:GCdonor_loss1.0000
1:39250104:G:GGdonor_gain1.0000
1:39250105:TGAG:Tdonor_loss1.0000
1:39250106:GAGCT:Gdonor_loss1.0000
1:39251939:GTA:Gdonor_gain1.0000
1:39254289:T:Aacceptor_gain1.0000
1:39254293:T:TAacceptor_gain1.0000
1:39254293:TGCA:Tacceptor_loss1.0000
1:39254295:CAG:Cacceptor_loss1.0000
1:39254296:A:AGacceptor_gain1.0000
1:39254297:G:GGacceptor_gain1.0000
1:39254297:GC:Gacceptor_gain1.0000
1:39254297:GCC:Gacceptor_gain1.0000
1:39254297:GCCC:Gacceptor_gain1.0000
1:39254297:GCCCC:Gacceptor_gain1.0000

AlphaMissense

49882 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:39231201:G:CQ80H1.000
1:39231201:G:TQ80H1.000
1:39231204:G:CK81N1.000
1:39231204:G:TK81N1.000
1:39231211:T:CF84L1.000
1:39231212:T:CF84S1.000
1:39231212:T:GF84C1.000
1:39231213:C:AF84L1.000
1:39231213:C:GF84L1.000
1:39231220:T:AW87R1.000
1:39231220:T:CW87R1.000
1:39231222:G:CW87C1.000
1:39231222:G:TW87C1.000
1:39231224:T:AV88D1.000
1:39250048:T:AL106Q1.000
1:39250048:T:CL106P1.000
1:39250051:G:CR107P1.000
1:39250056:G:CG109R1.000
1:39250056:G:TG109C1.000
1:39250057:G:AG109D1.000
1:39250057:G:TG109V1.000
1:39250066:T:AL112Q1.000
1:39250066:T:CL112P1.000
1:39250075:T:CL115P1.000
1:39250078:T:CL116S1.000
1:39250078:T:GL116W1.000
1:39250087:T:CL119P1.000
1:39254322:T:CF133L1.000
1:39254323:T:CF133S1.000
1:39254324:T:AF133L1.000

dbSNP variants (sampled 300 via entrez): RS1000004922 (1:39106878 G>C), RS1000008491 (1:39125029 C>T), RS1000028640 (1:39223629 C>T), RS1000028671 (1:39294129 C>A,T), RS1000029686 (1:39270424 A>G,T), RS1000045158 (1:39474643 G>A,C), RS1000046028 (1:39426844 T>G), RS1000059838 (1:39293901 T>G), RS1000061938 (1:39261264 CT>C), RS1000065095 (1:39115041 A>T), RS1000074861 (1:39259783 C>T), RS1000077717 (1:39170995 T>C), RS1000086648 (1:39263402 T>G), RS1000087748 (1:39216074 T>A), RS1000092915 (1:39119675 G>A)

Disease associations

OMIM: gene MIM:608271 | disease phenotypes: MIM:618325, MIM:100200, MIM:607432, MIM:213000

GenCC curated gene-disease

DiseaseClassificationInheritance
lissencephaly 9 with complex brainstem malformationStrongAutosomal dominant
autosomal dominant nonsyndromic hearing lossLimitedAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
lissencephaly spectrum disorder with complex brainstem malformationModerateAD

Mondo (11): lissencephaly 9 with complex brainstem malformation (MONDO:0032677), skeletal dysplasia (MONDO:0018230), prostate cancer (MONDO:0008315), cleft palate (MONDO:0016064), abducens nerve palsy (MONDO:0007033), epilepsy (MONDO:0005027), intellectual disability (MONDO:0001071), lissencephaly spectrum disorders (MONDO:0018838), isolated cerebellar hypoplasia/agenesis (MONDO:0008939), isolated unilateral hemispheric cerebellar hypoplasia (MONDO:0017112), autosomal dominant nonsyndromic hearing loss (MONDO:0019587)

Orphanet (9): Posterior-predominant lissencephaly-broad flat pons and medulla-midline crossing defects syndrome (Orphanet:572013), Primary bone dysplasia (Orphanet:364526), Familial prostate cancer (Orphanet:1331), Cleft palate (Orphanet:2014), Lissencephaly (Orphanet:48471), Isolated cerebellar agenesis (Orphanet:1398), Cerebellar hypoplasia-tapetoretinal degeneration syndrome (Orphanet:2246), Isolated unilateral hemispheric cerebellar hypoplasia (Orphanet:269218), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

49 total (30 of 49 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000011Neurogenic bladder
HP:0000252Microcephaly
HP:0000286Epicanthus
HP:0000316Hypertelorism
HP:0000324Facial asymmetry
HP:0000369Low-set ears
HP:0000486Strabismus
HP:0000609Optic nerve hypoplasia
HP:0000733Motor stereotypy
HP:0001250Seizure
HP:0001252Hypotonia
HP:0001257Spasticity
HP:0001263Global developmental delay
HP:0001302Pachygyria
HP:0001320Cerebellar vermis hypoplasia
HP:0001339Lissencephaly
HP:0001344Absent speech
HP:0001629Ventricular septal defect
HP:0002015Dysphagia
HP:0002069Bilateral tonic-clonic seizure
HP:0002079Hypoplasia of the corpus callosum
HP:0002365Hypoplasia of the brainstem
HP:0002384Focal impaired awareness seizure
HP:0002827Hip dislocation
HP:0003593Infantile onset
HP:0003621Juvenile onset
HP:0004305Involuntary movements
HP:0004322Short stature
HP:0005280Depressed nasal bridge

GWAS associations

39 associations (top):

StudyTraitp-value
GCST000755_20HDL cholesterol4.000000e-10
GCST002899_32HDL cholesterol8.000000e-10
GCST003420_1Colorectal cancer3.000000e-07
GCST003475_2Beard thickness8.000000e-06
GCST003619_8Type 2 diabetes2.000000e-09
GCST003773_11Loneliness (multivariate analysis)5.000000e-06
GCST004482_47Peripheral arterial disease (traffic-related air pollution interaction)1.000000e-06
GCST004482_78Peripheral arterial disease (traffic-related air pollution interaction)1.000000e-06
GCST004605_54Mean corpuscular hemoglobin concentration2.000000e-10
GCST004894_33Type 2 diabetes6.000000e-07
GCST004894_90Type 2 diabetes3.000000e-06
GCST005162_3Glucagon levels in response to oral glucose tolerance test (fasting)2.000000e-06
GCST005337_28Headache4.000000e-08
GCST005413_12Type 2 diabetes9.000000e-09
GCST006867_1Type 2 diabetes8.000000e-14
GCST006979_873Heel bone mineral density2.000000e-11
GCST007515_17Type 2 diabetes7.000000e-16
GCST007516_20Type 2 diabetes (adjusted for BMI)7.000000e-09
GCST007517_1Type 2 diabetes9.000000e-11
GCST007518_3Type 2 diabetes (adjusted for BMI)9.000000e-09
GCST007611_13Chronic obstructive pulmonary disease or high blood pressure (pleiotropy)7.000000e-09
GCST007656_12Chronic obstructive pulmonary disease or resting heart rate (pleiotropy)3.000000e-11
GCST008129_3Body mass index4.000000e-11
GCST009379_26Type 2 diabetes3.000000e-26
GCST009462_17Optic disc size1.000000e-08
GCST010118_2Type 2 diabetes3.000000e-11
GCST010173_83Triglyceride levels4.000000e-13
GCST010321_97PR interval4.000000e-14
GCST010696_14Cortical thickness (min-P)9.000000e-12
GCST010697_24Cortical surface area (min-P)2.000000e-08

EFO canonical traits (14, from GWAS)

EFO IDTrait name
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0007865loneliness measurement
EFO:0007908traffic air pollution measurement
EFO:0004528mean corpuscular hemoglobin concentration
EFO:0004307glucose tolerance test
EFO:0008463glucagon measurement
EFO:0009270heel bone mineral density
EFO:0004340body mass index
EFO:0004530triglyceride measurement
EFO:0004462PR interval
EFO:0004346neuroimaging measurement
EFO:0004840cortical thickness
EFO:0006935thalamus volume
EFO:0007984platelet component distribution width

MeSH disease descriptors (6)

DescriptorNameTree numbers
D002972Cleft PalateC05.500.460.185; C05.660.207.540.460.185; C07.320.440.185; C07.465.525.185; C07.650.500.460.185; C07.650.525.185; C16.131.621.207.540.460.185; C16.131.850.500.460.185; C16.131.850.525.185
D004827EpilepsyC10.228.140.490
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D054082LissencephalyC10.500.507.450.499; C16.131.666.507.450.499
D011471Prostatic NeoplasmsC04.588.945.440.770; C12.100.500.260.750; C12.100.500.565.625; C12.200.294.260.750; C12.200.294.565.625; C12.200.758.409.750; C12.900.619.750
C562568Cerebellar Hypoplasia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
methylmercuric chloridedecreases expression, increases expression4
Estradiolaffects expression, increases expression, increases reaction3
Valproic Acidaffects expression, decreases expression, decreases methylation3
Aflatoxin B1decreases methylation, affects expression3
bisphenol Adecreases expression, affects cotreatment, affects methylation, decreases methylation2
trichostatin Aaffects cotreatment, decreases expression2
methacrylaldehydeaffects cotreatment, decreases expression, increases oxidation, increases abundance2
bisphenol Saffects methylation, affects cotreatment, increases methylation, decreases expression2
Acroleinaffects cotreatment, decreases expression, increases oxidation, increases abundance2
Benzo(a)pyreneincreases methylation, affects methylation, decreases expression, decreases methylation2
Cisplatinaffects cotreatment, increases expression, affects response to substance2
Ozoneaffects cotreatment, decreases expression, increases oxidation, increases abundance2
Tretinoinaffects expression, increases expression2
FR900359affects phosphorylation, increases phosphorylation1
dicrotophosincreases expression1
testosterone enanthateaffects expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, decreases expression, increases oxidation, increases abundance1
lead acetateaffects cotreatment, increases expression1
titanium dioxidedecreases methylation1
pyrogallol 1,3-dimethyl etheraffects cotreatment, decreases expression, affects localization, increases expression1
decabromobiphenyl etherincreases expression1
arseniteaffects binding, decreases reaction1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
zinc protoporphyrinaffects cotreatment, increases expression1
sodium arseniteincreases stability1
potassium chromate(VI)affects cotreatment, decreases expression1
aflatoxin B2increases methylation1
coumarinaffects phosphorylation1
epigallocatechin gallateincreases expression, affects cotreatment, decreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00029224PHASE4COMPLETEDTreatment With Zoledronic Acid in Patients With Breast Cancer, Multiple Myeloma, and Prostate Cancer With Cancer Related Bone Lesions
NCT00035997PHASE4COMPLETEDOpen-label Trial on the Effect of I.V. Zoledronic Acid 4 mg on Bone Density in Hormone Sensitive Prostate Cancer Patients With Bone Metastasis
NCT00063609PHASE4COMPLETEDThe Effect of Zoledronic Acid on Bone Loss in Prostate Cancer Patients Undergoing Androgen Deprivation Therapy
NCT00103623PHASE4SUSPENDEDThe Plenaxis® Experience Study
NCT00106392PHASE4COMPLETEDA Safety and Efficacy Study of Prograf in the Prevention of Erectile Dysfunction After Radical Prostatectomy
NCT00185029PHASE4UNKNOWNMR-Lymphography and Lymph Node Staging in Prostate Cancer
NCT00199485PHASE4COMPLETEDAngelica Sinensis for the Treatment of Hot Flashes in Men Undergoing LHRH Therapy for Prostate Cancer
NCT00219219PHASE4COMPLETEDZoledronic Acid in the Prevention of Skeletal-related Events in Hormone Refractory and Hormone-sensitive Prostate Cancer Patients With Bone Metastases
NCT00219271PHASE4COMPLETEDEffect Of Zoledronic Acid On Circulating And Bone Marrow-Residing Prostate Cancer Cells In Patients With Clinically Localized Prostate Cancer
NCT00237146PHASE4COMPLETEDStudy to Evaluate Zoledronic Acid on Quality of Life and Skeletal-related Events as Adjuvant Treatment in Patients With Hormone-naïve Prostate Cancer and Bone Metastasis Who Have Undergone Orchiectomy
NCT00242554PHASE4COMPLETEDOpen-label Phase IV Clinical Trial to Evaluate the Safety and Tolerability of Zoledronic Acid in Patients With Prostate Cancer and Bone Metastases
NCT00280098PHASE4COMPLETEDDocetaxel in the Treatment of Hormone Refractory Prostate Cancer
NCT00293696PHASE4COMPLETEDCasodex/Zoladex Biomarkers in Localised Prostate Cancer
NCT00334139PHASE4COMPLETEDEffect of Zoledronic Acid on Bone Metabolism in Patients With Bone Metastasis and Prostate or Breast Cancer
NCT00375765PHASE4COMPLETEDEffects On Dihydrotestosterone Regulated Gene Expression In Benign Prostatic Hyperplasia Or Prostate Cancer
NCT00391690PHASE4COMPLETEDEvaluation of Bone Markers as Diagnostic Tools for Early Detection of Bone Metastases in Patients With High Risk Prostate Cancer
NCT00422708PHASE4COMPLETEDLocal Anesthesia for Prostate Biopsy
NCT00526331PHASE4COMPLETEDEvaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00590213PHASE4COMPLETEDCompare the Value of Prophylactic Versus Therapeutic Breast Radiotherapy in CASODEX
NCT00629330PHASE4TERMINATEDDissemination of Prostate Cancer Screening to PCP’s in African American Communities
NCT00771966PHASE4COMPLETEDRadical Prostatectomy and Perioperative Fluid Therapy
NCT00805701PHASE4COMPLETEDStudy Assessing The Efficacy And Safety Of Avodart (Dutasteride) At Improving Urinary Symptoms In Men With Prostate Cancer Who Are Undergoing Seed Implantation
NCT00859027PHASE4COMPLETEDEffect Of Risedronate On Bone Mass In Older Men Receiving Neoadjuvant Therapy For Prostate Cancer
NCT00906269PHASE4UNKNOWNCan Hyperbaric Oxygen Improve Erectile Function Following Surgery for Prostate Cancer
NCT00953277PHASE4COMPLETEDStudy of Nerve Reconstruction Using AVANCE in Subjects Who Undergo Robotic Assisted Prostatectomy for Treatment of Prostate Cancer
NCT00982800PHASE4COMPLETEDDoes Postoperative Gabapentin Reduce Pain, Opioid Consumption and Anxiety and Have a Positive Effect on Health Related Quality of Life After Radical Prostatectomy?
NCT01083199PHASE4COMPLETEDGlobal Performance Evaluation of the AMS CONTINUUM™ Device
NCT01136226PHASE4COMPLETEDEvaluate Recovery of Testosterone for Patients Using Eligard
NCT01161563PHASE4COMPLETEDRandomized Crossover Trial to Assess the Tolerability of Gonadotropin Releasing Hormone (GnRH) Analogue Administration
NCT01230905PHASE4COMPLETEDStudy to Monitor the Effects of Androgen Suppression Treatment on the Heart
NCT01296672PHASE4COMPLETED3 Month Finasteride Challenge Test Can Significantly Improve the Performance of Screening for Prostate Cancer
NCT01365143PHASE4TERMINATEDProspective Randomized Trial Comparing Robotic Versus Open Radical Prostatectomy
NCT01379742PHASE4UNKNOWNComparison of Between ThinSeed™ and OncoSeed™ for Permanent Prostate Brachytherapy
NCT01486563PHASE4COMPLETEDHydroxyethyl Starch and Renal Function After Radical Prostatectomy
NCT01511874PHASE4COMPLETEDEfficacy and Safety Study of ELIGARD 22.5mg With Prostate Cancer
NCT01512472PHASE4TERMINATEDFirmagon (Degarelix) Intermittent Therapy
NCT01547416PHASE4COMPLETEDThe Effect of Combined General/Epidural Anesthesia Versus General Anesthesia on Diaphragmatic Function
NCT01571544PHASE4COMPLETEDThe Use of Thermal Suits as Preventing Hypothermia During Surgery
NCT01581749PHASE4UNKNOWNEvaluation of Truebeam for Low-Intermediate Risk Prostate Cancer
NCT01649635PHASE4COMPLETEDStudy of Cabazitaxel Combined With Prednisone and Prophylaxis of Neutropenia Complications in the Treatment of Patients With Metastatic Castration-resistant Prostate Cancer