MYRF

gene
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Also known as Ndt80pqn-47MRF

Summary

MYRF (myelin regulatory factor, HGNC:1181) is a protein-coding gene on chromosome 11q12.2, encoding Myelin regulatory factor (Q9Y2G1). Constitutes a precursor of the transcription factor.

This gene encodes a transcription factor that is required for central nervous system myelination and may regulate oligodendrocyte differentiation. It is thought to act by increasing the expression of genes that effect myelin production but may also directly promote myelin gene expression. Loss of a similar gene in mouse models results in severe demyelination. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 745 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): cardiac-urogenital syndrome (Definitive, ClinGen) — +2 more curated relationships
  • GWAS associations: 142
  • Clinical variants (ClinVar): 363 total — 35 pathogenic, 33 likely-pathogenic
  • Phenotypes (HPO): 44
  • Transcription factor: yes — 12 downstream targets (CollecTRI)
  • MANE Select transcript: NM_001127392

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1181
Approved symbolMYRF
Namemyelin regulatory factor
Location11q12.2
Locus typegene with protein product
StatusApproved
AliasesNdt80, pqn-47, MRF
Ensembl geneENSG00000124920
Ensembl biotypeprotein_coding
OMIM608329
Entrez745

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 21 protein_coding, 6 retained_intron, 2 nonsense_mediated_decay

ENST00000265460, ENST00000278836, ENST00000389602, ENST00000536352, ENST00000537318, ENST00000537766, ENST00000539361, ENST00000546247, ENST00000675319, ENST00000675345, ENST00000675792, ENST00000856798, ENST00000856799, ENST00000856800, ENST00000856801, ENST00000856802, ENST00000856803, ENST00000856804, ENST00000856805, ENST00000856806, ENST00000856807, ENST00000856808, ENST00000856809, ENST00000856810, ENST00000856811, ENST00000856812, ENST00000856813, ENST00000918478, ENST00000918479

RefSeq mRNA: 2 — MANE Select: NM_001127392 NM_001127392, NM_013279

CCDS: CCDS31579, CCDS44622

Canonical transcript exons

ENST00000278836 — 27 exons

ExonStartEnd
ENSE000008516676177024661770525
ENSE000008516686176926061769321
ENSE000008516696176595861766221
ENSE000009164696177773461777845
ENSE000009164716177726461777464
ENSE000009164746177678761776877
ENSE000009164866177182961771952
ENSE000009164886177150061771750
ENSE000011401206177632261776432
ENSE000011967086175263661752790
ENSE000012286036178349861783600
ENSE000013245936176562561765712
ENSE000013574476177605661776132
ENSE000015063426177396761774162
ENSE000017261696178428061784385
ENSE000017571016178580061785874
ENSE000018033346178385161783925
ENSE000018062766177926361779423
ENSE000022686356178606361788518
ENSE000023192616177838061778489
ENSE000034625876178071261780792
ENSE000035023506178022261780290
ENSE000035067826178113861781329
ENSE000035267666177949861779570
ENSE000035292846178157361781824
ENSE000035684146177984261779930
ENSE000036426126178096061781045

Expression profiles

Bgee: expression breadth ubiquitous, 223 present calls, max score 99.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.4766 / max 1290.5938, expressed in 1002 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
11459722.83231000
1146000.3329152
1145990.199454
1146010.101654
1145980.01034

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
middle frontal gyrusUBERON:000270299.20gold quality
C1 segment of cervical spinal cordUBERON:000646998.81gold quality
inferior vagus X ganglionUBERON:000536398.71gold quality
spinal cordUBERON:000224098.64gold quality
inferior olivary complexUBERON:000212798.45gold quality
medulla oblongataUBERON:000189697.31gold quality
subthalamic nucleusUBERON:000190697.23gold quality
ventral tegmental areaUBERON:000269196.86gold quality
lateral globus pallidusUBERON:000247696.80gold quality
superior vestibular nucleusUBERON:000722796.25gold quality
dorsal motor nucleus of vagus nerveUBERON:000287096.22gold quality
dorsal plus ventral thalamusUBERON:000189796.20gold quality
midbrainUBERON:000189196.19gold quality
substantia nigra pars reticulataUBERON:000196696.17gold quality
pigmented layer of retinaUBERON:000178296.14gold quality
substantia nigraUBERON:000203896.09gold quality
corpus callosumUBERON:000233695.79gold quality
putamenUBERON:000187495.78gold quality
pylorusUBERON:000116695.44gold quality
gall bladderUBERON:000211095.24gold quality
globus pallidusUBERON:000187594.82gold quality
cranial nerve IIUBERON:000094194.76gold quality
Ammon’s hornUBERON:000195494.64gold quality
CA1 field of hippocampusUBERON:000388194.50gold quality
amygdalaUBERON:000187694.27gold quality
medial globus pallidusUBERON:000247794.20gold quality
right lungUBERON:000216794.16gold quality
body of pancreasUBERON:000115094.04gold quality
caudate nucleusUBERON:000187394.01gold quality
substantia nigra pars compactaUBERON:000196593.64gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-MTAB-6108yes122.62
E-GEOD-84465yes12.51
E-ANND-3yes4.33

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

12 targets.

TargetRegulation
ABCB1
ADAM2
CDR2
COL5A2
EIF3K
FGF2
MIR499A
MYF6
MYH7B
MYOG
SMARCA4
STAB1

miRNA regulators (miRDB)

142 targeting MYRF, 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-4673100.0066.641490
HSA-MIR-4283100.0066.422097
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-4481100.0066.421669
HSA-MIR-4692100.0067.322066
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-451499.9967.101870
HSA-MIR-4645-5P99.9865.811284
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-302E99.9670.742669
HSA-MIR-9-3P99.9670.882068
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-391099.9571.132227
HSA-MIR-185-3P99.9567.011743
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-5195-3P99.9270.921877
HSA-MIR-145-5P99.9271.131836
HSA-MIR-124-3P99.8973.743043
HSA-MIR-506-3P99.8973.553057
HSA-MIR-302A-3P99.8971.231777
HSA-MIR-302B-3P99.8971.231777

Literature-anchored findings (GeneRIF, showing 21)

  • A Bacteriophage tailspike domain promotes self-cleavage of a human membrane-bound transcription factor, the myelin regulatory factor MYRF. (PMID:23966832)
  • molecular mechanisms underlying the homo-trimerization of Myrf N-terminal fragments and the homo-trimeric DNA binding of Myrf N-terminal fragments (PMID:28160598)
  • The relative scarcity of oligodendrocyte lineage cells expressing MYRF in demyelinated MS lesions demonstrates, for the first time, that chronic lesions lack oligodendrocytes that express this necessary transcription factor for remyelination and supports the notion that a failure to fully differentiate underlies remyelination failure. (PMID:28631093)
  • Functional defects of MYRF are likely to be causally associated with encephalopathy with extensive myelin vacuolization (PMID:29265453)
  • Heterozygous variants in MYRF should be considered in patients with variants of Scimitar syndrome and urogenital anomalies. (PMID:29446546)
  • We identified four unrelated individuals with congenital diaphragmatic hernia with damaging de novo variants in MYRF (P = 5.3x10(-8)), including one likely gene-disrupting (LGD) and three deleterious missense (D-mis) variants. Eight additional individuals with de novo LGD or missense variants were identified from our other genetic studies or from the literature. (PMID:30532227)
  • The results suggest that MYRF is a novel causative gene of 46,XY and 46,XX disorders of sex development and MYRF is a transcription factor regulating coelomic epithelium and/or coelomic epithelium derived cells proliferation and migration, which is essential for development of multiple organs. (PMID:30985895)
  • Identified a canonical splice site alteration upstream of the last exon of the gene encoding myelin regulatory factor (MYRF c.3376-1G>A), which produced a stable RNA transcript, leading to a frameshift mutation p.Gly1126Valfs*31 in the C-terminus of the protein. (PMID:31048900)
  • results underline the importance of including SLC18A3 sequencing in the differential diagnostics of fetuses with arthrogryposis, FADS, or LMPS of unknown etiology (PMID:31069960)
  • These evidence all support that truncation mutations in the C-terminal region of MYRF are responsible for autosomal dominant high hyperopia in these families. (PMID:31172260)
  • This is the first trio-based whole-genome sequencing (WGS), study for nanophthalmos, revealing the potential role of de novo mutations (DNMs) in MYRF and rare inherited genetic variants in PRSS56 and MFRP. (PMID:31266062)
  • C-terminal variants in MYRF, which are expected to escape nonsense-mediated decay, represent a rare cause of autosomal dominant nanophthalmos with or without dextrocardia or congenital diaphragmatic hernia. (PMID:31700225)
  • Functional mechanism and pathogenic potential of MYRF ICA domain mutations implicated in birth defects. (PMID:31964908)
  • The genetic and clinical landscape of nanophthalmos and posterior microphthalmos in an Australian cohort. (PMID:32052405)
  • Pancreatic Cancer Cells Require the Transcription Factor MYRF to Maintain ER Homeostasis. (PMID:32997974)
  • Common Myelin Regulatory Factor Gene Variants Predisposing to Excellence in Sports. (PMID:33670313)
  • Functional mechanisms of MYRF DNA-binding domain mutations implicated in birth defects. (PMID:33798553)
  • MYRF: A Mysterious Membrane-Bound Transcription Factor Involved in Myelin Development and Human Diseases. (PMID:33864620)
  • Evaluation of MYRF as a candidate gene for primary angle closure glaucoma. (PMID:35136345)
  • Truncation mutations in MYRF underlie primary angle closure glaucoma. (PMID:36129575)
  • Two sisters with cardiac-urogenital syndrome secondary to pathogenic splicing variant in the MYRF gene with unaffected parents: A case of gonadal mosaicism? (PMID:36695166)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriomyrfENSDARG00000078676
mus_musculusMyrfENSMUSG00000036098
rattus_norvegicusMyrfENSRNOG00000028274
drosophila_melanogasterCG3328FBGN0034985
caenorhabditis_elegansWBGENE00004134
caenorhabditis_elegansWBGENE00008999

Paralogs (1): MYRFL (ENSG00000166268)

Protein

Protein identifiers

Myelin regulatory factorQ9Y2G1 (reviewed: Q9Y2G1)

Alternative names: Myelin gene regulatory factor

All UniProt accessions (4): Q9Y2G1, A0A6Q8PFL7, A0A6Q8PFY9, A0A6Q8PHM1

UniProt curated annotations — full annotation on UniProt →

Function. Constitutes a precursor of the transcription factor. Mediates the autocatalytic cleavage that releases the Myelin regulatory factor, N-terminal component that specifically activates transcription of central nervous system (CNS) myelin genes. Membrane-bound part that has no transcription factor activity and remains attached to the endoplasmic reticulum membrane following cleavage. Transcription factor that specifically activates expression of myelin genes such as MBP, MOG, MAG, DUSP15 and PLP1 during oligodendrocyte (OL) maturation, thereby playing a central role in oligodendrocyte maturation and CNS myelination. Specifically recognizes and binds DNA sequence 5’-CTGGYAC-3’ in the regulatory regions of myelin-specific genes and directly activates their expression. Not only required during oligodendrocyte differentiation but is also required on an ongoing basis for the maintenance of expression of myelin genes and for the maintenance of a mature, viable oligodendrocyte phenotype.

Subunit / interactions. Homotrimer. Interacts (via C-terminal region) with TMEM98; the interaction inhibits MYRF self-cleavage.

Subcellular location. Endoplasmic reticulum membrane Nucleus. Cytoplasm Endoplasmic reticulum membrane.

Tissue specificity. Expressed in lung, brainstem, uterus and, to a lesser extent, in basal ganglion and liver. Weakly expressed in cerebellum. High expression detected in the retinal pigment epithelium, choroid, and optic nerve.

Post-translational modifications. Glycosylated. Follows autocatalytic cleavage via the peptidase S74 domain. Autoprocessing is apparently constitutive and is essential for transcriptional activity. Autocatalytic cleavage is inhibited by interaction with TMEM98.

Disease relevance. Encephalitis/encephalopathy, mild, with reversible myelin vacuolization (MMERV) [MIM:618113] An autosomal dominant disease characterized by episodes of acute encephalitis associated with impaired consciousness, delirious behavior, seizures, and reversible splenial lesions observed on diffusion magnetic resonance imaging. Most patients completely recover and there are no neurologic sequelae. MMERV occurs in children and is frequently associated with a trigger, such as a febrile illness. The disease may be caused by variants affecting the gene represented in this entry. Cardiac-urogenital syndrome (CUGS) [MIM:618280] An autosomal dominant syndrome characterized by partial anomalous pulmonary venous return, tracheal anomalies, pulmonary hypoplasia, congenital diaphragmatic hernia, thyroid fibrosis, thymic involution, cleft spleen, penoscrotal hypospadias, and cryptorchidism. The disease is caused by variants affecting the gene represented in this entry. Nanophthalmos 1 (NNO1) [MIM:600165] A form of nanophthalmos, a disorder of eye development characterized by extreme hyperopia and small functional eyes. The cornea and lens are normal in size and shape. Hyperopia occurs because insufficient growth along the visual axis places these lensing components too close to the retina. Nanophthalmic eyes show considerable thickening of both the choroidal vascular bed and scleral coat, which provide nutritive and structural support for the retina. NNO1 inheritance is autosomal dominant. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The nuclear localization signals mediate translocation to the nucleus. The peptidase S74 domain, also named Intramolecular Chaperone Auto-processed (ICA) domain or Intramolecular Chaperone Domain (ICD), has protease activity and mediates autocatalytic processing of the protein to generate the Myelin regulatory factor, N-terminal active transcription factor and the Myelin regulatory factor, C-terminal components.

Similarity. Belongs to the MRF family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9Y2G1-11yes
Q9Y2G1-22

RefSeq proteins (2): NP_001120864, NP_037411 (=MANE)

Domains & families (InterPro)

IDNameType
IPR008967p53-like_TF_DNA-bd_sfHomologous_superfamily
IPR024061NDT80_DNA-bd_domDomain
IPR025719MYRF_C2Domain
IPR026932MYRF_ICADomain
IPR030392S74_ICADomain
IPR037141NDT80_DNA-bd_dom_sfHomologous_superfamily
IPR051577MRF-likeFamily

Pfam: PF05224, PF13884, PF13887, PF13888

UniProt features (73 total): strand 18, mutagenesis site 10, sequence variant 9, region of interest 5, compositionally biased region 5, glycosylation site 4, chain 3, splice variant 3, sequence conflict 3, short sequence motif 2, topological domain 2, turn 2, coiled-coil region 1, site 1, modified residue 1, transmembrane region 1, helix 1, domain 1, DNA-binding region 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
5YHUX-RAY DIFFRACTION1.85
5ZHUX-RAY DIFFRACTION2.2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y2G1-F161.760.29

Functional residue map

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

Catalytic / active sites (1): 586–587 (cleavage; by autolysis)

Post-translational modifications (1): 123

Glycosylation sites (4): 919, 1043, 1065, 1129

Mutagenesis-validated functional residues (10):

PositionPhenotype
454decreased affinity for dna.
478decreased affinity for dna.
530decreased affinity for dna.
587prevents autocatalytic cleavage and generation of myelin regulatory factor, n-terminal part.
588reduces autocatalytic cleavage and generation of myelin regulatory factor, n-terminal part.
592prevents autocatalytic cleavage and generation of myelin regulatory factor, n-terminal part.
608does not affect autocatalytic cleavage.
635reduces autocatalytic cleavage and generation of myelin regulatory factor, n-terminal part.
688does not affect autocatalytic cleavage.
699prevents autocatalytic cleavage and generation of myelin regulatory factor, n-terminal part.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 341 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, RNGTGGGC_UNKNOWN, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_RESPONSE_TO_COCAINE, GOBP_RESPONSE_TO_IMMOBILIZATION_STRESS, TGCACTT_MIR519C_MIR519B_MIR519A, CROONQUIST_NRAS_SIGNALING_DN, ASTON_MAJOR_DEPRESSIVE_DISORDER_DN, GOBP_POSITIVE_REGULATION_OF_GLIAL_CELL_DIFFERENTIATION, GOBP_PLASMA_MEMBRANE_ORGANIZATION, GOBP_GLIAL_CELL_DEVELOPMENT, FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_DN, GOBP_NEUROGENESIS, CREBP1_Q2

GO Biological Process (14): oligodendrocyte development (GO:0014003), protein autoprocessing (GO:0016540), central nervous system myelination (GO:0022010), positive regulation of myelination (GO:0031643), central nervous system myelin maintenance (GO:0032286), response to immobilization stress (GO:0035902), response to cocaine (GO:0042220), positive regulation of DNA-templated transcription (GO:0045893), oligodendrocyte differentiation (GO:0048709), positive regulation of oligodendrocyte differentiation (GO:0048714), regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), proteolysis (GO:0006508), cell differentiation (GO:0030154)

GO Molecular Function (7): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription factor activity (GO:0003700), peptidase activity (GO:0008233), identical protein binding (GO:0042802), sequence-specific DNA binding (GO:0043565), DNA binding (GO:0003677), hydrolase activity (GO:0016787)

GO Cellular Component (9): nucleus (GO:0005634), nucleoplasm (GO:0005654), endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), cytosol (GO:0005829), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), endomembrane system (GO:0012505), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
regulation of DNA-templated transcription3
intracellular membrane-bounded organelle3
cytoplasm3
oligodendrocyte differentiation2
myelination2
DNA-templated transcription2
endomembrane system2
glial cell development1
protein processing1
oligodendrocyte development1
axon ensheathment in central nervous system1
regulation of myelination1
positive regulation of nervous system process1
positive regulation of cellular process1
central nervous system myelination1
myelin maintenance1
response to stress1
response to alkaloid1
response to oxygen-containing compound1
positive regulation of RNA biosynthetic process1
central nervous system development1
glial cell differentiation1
positive regulation of glial cell differentiation1
regulation of oligodendrocyte differentiation1
regulation of gene expression1
regulation of RNA biosynthetic process1
transcription by RNA polymerase II1
protein metabolic process1
cellular developmental process1
chromatin1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
transcription cis-regulatory region binding1
transcription regulator activity1
hydrolase activity1
catalytic activity, acting on a protein1
protein binding1
DNA binding1

Protein interactions and networks

STRING

930 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MYRFBEST1O76090832
MYRFSOX10P56693787
MYRFFEN1P39748774
MYRFTMEM98Q9Y2Y6757
MYRFPLP1P04400741
MYRFSPO11Q9Y5K1703
MYRFOLIG1Q8TAK6693
MYRFOLIG2Q13516683
MYRFMBPP02686613
MYRFNKX2-2O95096609
MYRFRFFLQ8WZ73597
MYRFREC8O95072578
MYRFMOBPQ13875565
MYRFFA2HQ7L5A8551
MYRFENPP6Q6UWR7546

IntAct

24 interactions, top by confidence:

ABTypeScore
PDGFRBPIK3R2psi-mi:“MI:0914”(association)0.610
GRAMD2BEFCAB14psi-mi:“MI:0914”(association)0.530
CTLA4B4GALT5psi-mi:“MI:0914”(association)0.530
KCNE3RIOK3psi-mi:“MI:0914”(association)0.530
NS3C15orf61psi-mi:“MI:0914”(association)0.350
SHTN1psi-mi:“MI:0914”(association)0.350
TMEM223psi-mi:“MI:0914”(association)0.350
TNFRSF10Apsi-mi:“MI:0914”(association)0.350
PCDHB3ESYT2psi-mi:“MI:0914”(association)0.350
KCNE3TMEM131Lpsi-mi:“MI:0914”(association)0.350
GPRC5BTNFRSF10Apsi-mi:“MI:0914”(association)0.350
ACKR3PDE2Apsi-mi:“MI:0914”(association)0.350
CHRNB1CLGNpsi-mi:“MI:0914”(association)0.350
DLK1PLPP3psi-mi:“MI:0914”(association)0.350
FYNMYCBP2psi-mi:“MI:0914”(association)0.350
MICBLGALS8psi-mi:“MI:0914”(association)0.350
OSTM1ASMTLpsi-mi:“MI:0914”(association)0.350
PCDHGA5UPK3BL1psi-mi:“MI:0914”(association)0.350
PRMT2DIAPH2psi-mi:“MI:0914”(association)0.350
TMEM98PDGFRBpsi-mi:“MI:0914”(association)0.350
TNFSF13FADS1psi-mi:“MI:0914”(association)0.350
ZDHHC11NRP1psi-mi:“MI:0914”(association)0.350

BioGRID (25): MYRF (Proximity Label-MS), MYRF (Affinity Capture-MS), MYRF (Affinity Capture-MS), MYRF (Affinity Capture-MS), MYRF (Affinity Capture-MS), MYRF (Affinity Capture-MS), MYRF (Proximity Label-MS), MYRF (Proximity Label-MS), MYRF (Proximity Label-MS), MYRF (Proximity Label-MS), MYRF (Proximity Label-MS), MYRF (Proximity Label-MS), MYRF (Proximity Label-MS), MYRF (Proximity Label-MS), MYRF (Affinity Capture-MS)

ESM2 similar proteins: A1YFY6, A2T6X9, A6H7I8, B2RUJ5, F1M5F3, F1N2W9, O35430, O35431, O95487, O95628, O95644, P0C6S7, P14316, P17863, P22681, P22682, P23798, P23906, P35227, P81133, P98084, Q02410, Q0IHY4, Q13469, Q14190, Q14432, Q1L994, Q3UR85, Q52L14, Q5CD77, Q5RD33, Q60591, Q61045, Q61079, Q66JB6, Q69ZT9, Q6NRE7, Q6QB00, Q8BIZ1, Q8BT14

Diamond homologs: D9PTN5, G5EFI7, Q1ZXA9, Q3UN70, Q3UR85, Q54B29, Q66IV1, Q9Y2G1, F1N4M2, Q54PT9, Q96LU7, B0FIH7

SIGNOR signaling

1 interactions.

AEffectBMechanism
MAP2K1“down-regulates activity”MYRFphosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic35
Likely pathogenic33
Uncertain significance186
Likely benign43
Benign31

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1013323NM_001127392.3(MYRF):c.1705G>T (p.Glu569Ter)Pathogenic
1176284NM_001127392.3(MYRF):c.350del (p.Gly117fs)Pathogenic
1180013NM_001127392.3(MYRF):c.1072C>T (p.Gln358Ter)Pathogenic
1698932NM_001127392.3(MYRF):c.648C>A (p.Tyr216Ter)Pathogenic
1710281NM_001127392.3(MYRF):c.428del (p.Gly143fs)Pathogenic
2307379NM_001127392.3(MYRF):c.1207C>T (p.Gln403Ter)Pathogenic
2441925NM_001127392.3(MYRF):c.1543C>T (p.Gln515Ter)Pathogenic
2582895NM_001127392.3(MYRF):c.871C>T (p.Arg291Ter)Pathogenic
2584483NM_001127392.3(MYRF):c.2956C>T (p.Arg986Ter)Pathogenic
2633042NM_001127392.3(MYRF):c.492_493del (p.Glu164fs)Pathogenic
3030545NM_001127392.3(MYRF):c.1208A>T (p.Gln403Leu)Pathogenic
3235908NM_001127392.3(MYRF):c.135-119_1062delPathogenic
3346708NM_001127392.3(MYRF):c.1948A>T (p.Lys650Ter)Pathogenic
3772320NM_001127392.3(MYRF):c.148_152del (p.Ile50fs)Pathogenic
3777343NM_001127392.3(MYRF):c.1116-3C>GPathogenic
3894587NM_001127392.3(MYRF):c.3376-1G>APathogenic
3894588MYRF, 1-BP DUP, 769CPathogenic
3894589MYRF, 1-BP DEL, 789C (rs769274302)Pathogenic
3894590MYRF, 1-BP DUP, 789C (rs769274302)Pathogenic
3894591MYRF, ARG478PROPathogenic
3894592MYRF, ARG986TERPathogenic
4072342NM_001127392.3(MYRF):c.3091del (p.Gln1031fs)Pathogenic
4536237NM_001127392.3(MYRF):c.278del (p.Pro93fs)Pathogenic
4537406NM_001127392.3(MYRF):c.1134_1135del (p.Val379fs)Pathogenic
560883NM_001127392.3(MYRF):c.1208A>G (p.Gln403Arg)Pathogenic
599372NM_001127392.3(MYRF):c.2518C>T (p.Arg840Ter)Pathogenic
599373NM_001127392.3(MYRF):c.1254_1255dup (p.Thr419fs)Pathogenic
620313NM_001127392.3(MYRF):c.2817G>A (p.Trp939Ter)Pathogenic
635185NM_001127392.3(MYRF):c.3361del (p.Arg1121fs)Pathogenic
635274NM_001127392.3(MYRF):c.3118A>G (p.Arg1040Gly)Pathogenic

SpliceAI

5119 predictions. Top by Δscore:

VariantEffectΔscore
11:61765620:TGCA:Tacceptor_loss1.0000
11:61765622:CAGGC:Cacceptor_loss1.0000
11:61765623:A:AGacceptor_gain1.0000
11:61765624:G:GAacceptor_gain1.0000
11:61765624:GGC:Gacceptor_gain1.0000
11:61765624:GGCC:Gacceptor_gain1.0000
11:61765696:G:GTdonor_gain1.0000
11:61765699:G:GTdonor_gain1.0000
11:61765708:GACCT:Gdonor_gain1.0000
11:61765709:ACCT:Adonor_gain1.0000
11:61765710:CCT:Cdonor_gain1.0000
11:61765711:CT:Cdonor_gain1.0000
11:61765711:CTGT:Cdonor_loss1.0000
11:61765712:TGTG:Tdonor_loss1.0000
11:61765713:G:GGdonor_gain1.0000
11:61765714:T:Adonor_loss1.0000
11:61765715:G:GCdonor_loss1.0000
11:61770518:GGAGC:Gdonor_gain1.0000
11:61770519:GAGC:Gdonor_gain1.0000
11:61770521:GC:Gdonor_gain1.0000
11:61770521:GCTGA:Gdonor_gain1.0000
11:61770522:C:Gdonor_gain1.0000
11:61770524:GA:Gdonor_gain1.0000
11:61770526:G:GGdonor_gain1.0000
11:61770530:GAC:Gdonor_gain1.0000
11:61771827:AG:Aacceptor_gain1.0000
11:61771828:GG:Gacceptor_gain1.0000
11:61771828:GGCC:Gacceptor_gain1.0000
11:61771948:GAGCT:Gdonor_gain1.0000
11:61771950:GCT:Gdonor_gain1.0000

AlphaMissense

7511 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:61771889:T:AI351N1.000
11:61771894:T:AW353R1.000
11:61771894:T:CW353R1.000
11:61771895:G:CW353S1.000
11:61771896:G:CW353C1.000
11:61771896:G:TW353C1.000
11:61771918:T:AW361R1.000
11:61771918:T:CW361R1.000
11:61773980:T:GY377D1.000
11:61773987:T:AV379E1.000
11:61773993:C:AA381E1.000
11:61773995:G:CD382H1.000
11:61773996:A:TD382V1.000
11:61773998:A:CK383Q1.000
11:61773998:A:GK383E1.000
11:61773999:A:CK383T1.000
11:61773999:A:TK383M1.000
11:61774000:G:CK383N1.000
11:61774000:G:TK383N1.000
11:61774001:G:AG384S1.000
11:61774001:G:CG384R1.000
11:61774001:G:TG384C1.000
11:61774002:G:AG384D1.000
11:61774002:G:TG384V1.000
11:61774004:T:CF385L1.000
11:61774005:T:CF385S1.000
11:61774005:T:GF385C1.000
11:61774006:C:AF385L1.000
11:61774006:C:GF385L1.000
11:61774010:T:CF387L1.000

dbSNP variants (sampled 300 via entrez): RS1000172133 (11:61763613 C>T), RS1000224871 (11:61764357 A>G), RS1000238769 (11:61760489 G>T), RS1000401284 (11:61776361 G>A,C,T), RS1000478188 (11:61775184 G>A), RS1000557222 (11:61763386 C>T), RS1000636503 (11:61782241 C>A,T), RS1000736421 (11:61774877 C>T), RS1000754972 (11:61789019 T>A,C), RS1000955626 (11:61754068 G>A), RS1000987448 (11:61782644 G>A,T), RS1001069074 (11:61760191 A>C), RS1001207069 (11:61759586 C>T), RS1001280833 (11:61759913 T>C), RS1001445514 (11:61764130 G>C,T)

Disease associations

OMIM: gene MIM:608329 | disease phenotypes: MIM:618113, MIM:618280, MIM:600165, MIM:142340, MIM:236750

GenCC curated gene-disease

DiseaseClassificationInheritance
cardiac-urogenital syndromeStrongAutosomal dominant
hyperopiaStrongAutosomal dominant
encephalitis/encephalopathy, mild, with reversible myelin vacuolizationLimitedAutosomal dominant

ClinGen Gene-Disease Validity (1)

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

DiseaseClassificationInheritance
cardiac-urogenital syndromeDefinitiveAD

Mondo (12): encephalitis/encephalopathy, mild, with reversible myelin vacuolization (MONDO:0020853), cardiac-urogenital syndrome (MONDO:0032653), disorder of sexual differentiation (MONDO:0002145), scimitar syndrome (MONDO:0015987), prostate cancer (MONDO:0008315), neurodevelopmental disorder (MONDO:0700092), nanophthalmos 1 (MONDO:0010836), congenital diaphragmatic hernia (MONDO:0005711), urogenital tract malformation (MONDO:0019356), non-immune hydrops fetalis (MONDO:0009369), dextrocardia (MONDO:0015661), hyperopia (MONDO:0004891)

Orphanet (9): Cardiac-urogenital syndrome (Orphanet:647811), Difference of sex development (Orphanet:90771), Scimitar syndrome (Orphanet:185), Familial prostate cancer (Orphanet:1331), Nanophthalmos (Orphanet:35612), Congenital diaphragmatic hernia (Orphanet:2140), Urogenital tract malformation (Orphanet:83001), Non-immune hydrops fetalis (Orphanet:363999), Dextrocardia (Orphanet:1666)

HPO phenotypes

44 total (30 of 44 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000028Cryptorchidism
HP:0000048Bifid scrotum
HP:0000054Micropenis
HP:0000062Ambiguous genitalia
HP:0000105Enlarged kidney
HP:0000151Aplasia of the uterus
HP:0000431Wide nasal bridge
HP:0000776Congenital diaphragmatic hernia
HP:0000808Penoscrotal hypospadias
HP:0001249Intellectual disability
HP:0001250Seizure
HP:0001270Motor delay
HP:0001629Ventricular septal defect
HP:0001631Atrial septal defect
HP:0001636Tetralogy of Fallot
HP:0001643Patent ductus arteriosus
HP:0001649Tachycardia
HP:0001651Dextrocardia
HP:0001698Pericardial effusion
HP:0001747Accessory spleen
HP:0002089Pulmonary hypoplasia
HP:0002566Intestinal malrotation
HP:0002779Tracheomalacia
HP:0002780Bronchomalacia
HP:0003010Prolonged bleeding time
HP:0003621Juvenile onset
HP:0004383Hypoplastic left ventricle
HP:00046912-3 toe syndactyly
HP:0006846Acute encephalopathy

GWAS associations

142 associations (top):

StudyTraitp-value
GCST001178_6Plasma omega-3 polyunsaturated fatty acid level (eicosapentaenoic acid)6.000000e-58
GCST001179_1Plasma omega-3 polyunsaturated fatty acid levels (docosapentaenoic acid)1.000000e-151
GCST001180_3Plasma omega-3 polyunsaturated fatty acid levels (alphalinolenic acid)1.000000e-63
GCST001725_11Inflammatory bowel disease2.000000e-15
GCST001834_5Oleic acid (18:1n-9) levels2.000000e-32
GCST001841_1Palmitoleic acid (16:1n-7) levels7.000000e-13
GCST002444_5Plasma omega-6 polyunsaturated fatty acid levels (dihomo-gamma-linolenic acid)5.000000e-168
GCST002446_1Plasma omega-6 polyunsaturated fatty acid levels (linoleic acid)4.000000e-274
GCST002446_7Plasma omega-6 polyunsaturated fatty acid levels (linoleic acid)3.000000e-21
GCST002448_6Plasma omega-6 polyunsaturated fatty acid levels (adrenic acid)4.000000e-140
GCST002449_6Plasma omega-6 polyunsaturated fatty acid levels (arachidonic acid)0.000000e+00
GCST002449_8Plasma omega-6 polyunsaturated fatty acid levels (arachidonic acid)7.000000e-147
GCST002450_8Plasma omega-6 polyunsaturated fatty acid levels (gamma-linolenic acid)2.000000e-72
GCST002454_8Colorectal cancer9.000000e-21
GCST002457_3P wave duration3.000000e-08
GCST002712_12Red blood cell fatty acid levels2.000000e-12
GCST002712_2Red blood cell fatty acid levels8.000000e-90
GCST002712_3Red blood cell fatty acid levels1.000000e-09
GCST002712_4Red blood cell fatty acid levels3.000000e-305
GCST002712_7Red blood cell fatty acid levels3.000000e-19
GCST002712_8Red blood cell fatty acid levels2.000000e-10
GCST002712_9Red blood cell fatty acid levels6.000000e-43
GCST003818_34Resting heart rate2.000000e-30
GCST004132_88Crohn’s disease9.000000e-07
GCST004139_2Bipolar disorder1.000000e-10
GCST004139_22Bipolar disorder6.000000e-09
GCST004571_28Iron status biomarkers (total iron binding capacity)5.000000e-08
GCST004572_9Iron status biomarkers (transferrin saturation)5.000000e-08
GCST004601_157Red blood cell count4.000000e-21
GCST004602_195Mean corpuscular volume7.000000e-11

EFO canonical traits (31, from GWAS)

EFO IDTrait name
EFO:0007760eicosapentaenoic acid measurement
EFO:0006809docosapentaenoic acid measurement
EFO:0007759alpha-linolenic acid measurement
EFO:0005680omega-6 polyunsaturated fatty acid measurement
EFO:0005094P wave duration
EFO:0006810oleic acid measurement
EFO:0006808arachidonic acid measurement
EFO:0006807linoleic acid measurement
EFO:0006811linolenic acid measurement
EFO:0006334total iron binding capacity
EFO:0004305erythrocyte count
EFO:0004348hematocrit
EFO:0004509hemoglobin measurement
EFO:0007986reticulocyte count
EFO:0007764delta-5 desaturase measurement
EFO:0009131response to polyunsaturated fatty acid supplementation
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004530triglyceride measurement
EFO:0009594irritability measurement
EFO:0009270heel bone mineral density
EFO:0003924hair color
EFO:1002011adult onset asthma
EFO:0009963bipolar I disorder
EFO:0004469HOMA-B
EFO:0010382phosphatidylcholine 36:4 measurement
EFO:0010118sphingomyelin measurement
EFO:0005059acylcarnitine measurement
EFO:0006944systolic blood pressure change measurement
EFO:0010119omega-3 polyunsaturated fatty acid measurement
EFO:0004346neuroimaging measurement

MeSH disease descriptors (8)

DescriptorNameTree numbers
D003914DextrocardiaC14.240.400.280; C14.280.400.280; C16.131.240.400.280; C16.131.810.250
D012734Disorders of Sex DevelopmentC12.050.351.875.253; C12.200.706.316; C12.800.316; C16.131.939.316; C19.391.119
D065630Hernias, Diaphragmatic, CongenitalC16.131.433; C23.300.707.960.500.116
D006956HyperopiaC11.744.479
D065886Neurodevelopmental DisordersF03.625
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
D012587Scimitar SyndromeC08.381.844; C08.695.815; C14.240.850.968; C14.907.780; C16.131.240.850.937; C16.131.740.815
C563983Nanophthalmos 1 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Acetaminophendecreases expression2
Benzo(a)pyreneincreases methylation, increases expression2
Cisplatinincreases expression, affects response to substance, affects cotreatment2
Aflatoxin B1decreases methylation, increases methylation2
FR900359decreases phosphorylation1
dicrotophosincreases expression1
methyleugenolincreases expression1
bisphenol Aincreases expression1
cobaltous chloridedecreases expression1
butyraldehydedecreases expression1
benzo(e)pyreneincreases methylation1
2-palmitoylglycerolincreases expression1
abrinedecreases expression1
jinfukangaffects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
Capecitabineincreases response to substance1
Sunitinibdecreases expression1
Arsenicaffects methylation1
Vehicle Emissionsincreases abundance, increases expression1
Caffeineincreases phosphorylation1
Leadaffects methylation1
Methapyrileneincreases methylation1
Niclosamideincreases expression1
Silicon Dioxidedecreases expression1
Smokedecreases expression1
Tobacco Smoke Pollutionaffects expression1
Triclosanincreases expression1
Antirheumatic Agentsincreases expression1
Vitamin K 3affects expression1
Particulate Matterincreases abundance, increases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00347204PHASE4COMPLETEDComparison of Acular LS Versus Nevanac for Pain Control in Eyes Undergoing PRK
NCT00455455PHASE4COMPLETEDCorneal and Conjunctival Sensitivity and Staining Study
NCT00937105PHASE4COMPLETEDDaily Wear Corneal Infiltrative Event Study
NCT01387360PHASE4COMPLETEDPresbyopic Supracor Treatment for Near Myopic/Hyperopic Pseudophakic Eyes
NCT01977807PHASE4UNKNOWNA Prospective Safety and Effectiveness Study of the 500 Hz Technolas Perfect Vision Excimer Laser in Asian Eyes Using LASIK
NCT02071576PHASE4UNKNOWNA Prospective Safety and Effectiveness Study of the 500 Hz Technolas Perfect Vision Excimer Laser Using LASIK
NCT02112968PHASE4UNKNOWNA Prospective Safety and Effectiveness Study of a New High Repetition Rate Excimer Laser Using LASIK for the Correction of Ammetropia and Presbyopia
NCT03881670PHASE4COMPLETEDOn-Eye Optical Quality of Lotrafilcon B Lenses Over 12 Hours
NCT04208750PHASE4COMPLETEDClinical Investigation of the Vision-R800 Device.
NCT04283331PHASE4UNKNOWNAnesthetic Impregnated Bandage Soft Contact Lens (BSCL) in Pain Management After Photorefractive Keratectomy (PRK)
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