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Aliases for GFER Gene

Aliases for GFER Gene

  • Growth Factor, Augmenter Of Liver Regeneration 2 3 5
  • FAD-Linked Sulfhydryl Oxidase ALR 2 3
  • HERV1 3 4
  • ALR 3 4
  • HPO 3 4
  • Growth Factor, Erv1 (S. Cerevisiae)-Like (Augmenter Of Liver Regeneration) 2
  • Hepatic Regenerative Stimulation Substance 3
  • Augmenter Of Liver Regeneration 4
  • ERV1 Homolog (S. Cerevisiae) 2
  • Erv1-Like Growth Factor 3
  • Hepatopoietin Protein 3
  • Hepatopoietin 4
  • ERV1 Homolog 3
  • EC 1.8.3.2 4
  • ERV1 3
  • HPO1 3
  • HPO2 3
  • HSS 3

External Ids for GFER Gene

Previous GeneCards Identifiers for GFER Gene

  • GC16P002051
  • GC16P002061
  • GC16P001974
  • GC16P002036
  • GC16P001965
  • GC16P002043
  • GC16P002045
  • GC16P002049
  • GC16P002056
  • GC16P002083
  • GC16P002095
  • GC16P002116

Summaries for GFER Gene

Entrez Gene Summary for GFER Gene

  • The hepatotrophic factor designated augmenter of liver regeneration (ALR) is thought to be one of the factors responsible for the extraordinary regenerative capacity of mammalian liver. It has also been called hepatic regenerative stimulation substance (HSS). The gene resides on chromosome 16 in the interval containing the locus for polycystic kidney disease (PKD1). The putative gene product is 42% similar to the scERV1 protein of yeast. The yeast scERV1 gene had been found to be essential for oxidative phosphorylation, the maintenance of mitochondrial genomes, and the cell division cycle. The human gene is both the structural and functional homolog of the yeast scERV1 gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for GFER Gene

GFER (Growth Factor, Augmenter Of Liver Regeneration) is a Protein Coding gene. Diseases associated with GFER include Myopathy, Mitochondrial Progressive, With Congenital Cataract, Hearing Loss, And Developmental Delay and Mitochondrial Metabolism Disease. Among its related pathways are Apoptotic Pathways in Synovial Fibroblasts and PAK Pathway. Gene Ontology (GO) annotations related to this gene include growth factor activity and protein disulfide oxidoreductase activity.

UniProtKB/Swiss-Prot for GFER Gene

  • Isoform 1: FAD-dependent sulfhydryl oxidase that regenerates the redox-active disulfide bonds in CHCHD4/MIA40, a chaperone essential for disulfide bond formation and protein folding in the mitochondrial intermembrane space. The reduced form of CHCHD4/MIA40 forms a transient intermolecular disulfide bridge with GFER/ERV1, resulting in regeneration of the essential disulfide bonds in CHCHD4/MIA40, while GFER/ERV1 becomes re-oxidized by donating electrons to cytochrome c or molecular oxygen.

  • Isoform 2: May act as an autocrine hepatotrophic growth factor promoting liver regeneration.

Gene Wiki entry for GFER Gene

Additional gene information for GFER Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GFER Gene

Genomics for GFER Gene

GeneHancer (GH) Regulatory Elements for GFER Gene

Promoters and enhancers for GFER Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16I001982 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 563.9 +0.3 338 3.3 HNRNPUL1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B YY1 GFER NOXO1 ENSG00000255513 ENSG00000261505 SRRM2 LOC105371055 UBE2I ENSG00000260954 TRAF7 ENSG00000260051
GH16I001981 Enhancer 0.7 ENCODE dbSUPER 559.1 -1.9 -1931 0.5 ZNF146 POLR2A GLIS1 NBN PRDM10 EZH2 GFER NOXO1 TBL3
GH16I002003 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 8.6 +23.1 23072 7.8 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF598 CRAMP1 ENSG00000261505 TBL3 ENSG00000255513 SRRM2 ENSG00000260051 SNORA64 TELO2 ENSG00000260954
GH16I001989 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 9.7 +7.8 7834 4.4 HDGF PKNOX1 FOXA2 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 ZNF263 ENSG00000261790 SYNGR3 ENSG00000255513 GFER ZNF598 MAPK8IP3 SPSB3 EME2 ENSG00000260107
GH16I001976 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 8.3 -4.8 -4842 4.9 MAX EBF1 E2F1 ZFHX2 POLR2A ATF7 KLF8 DEK CHD2 EGR2 NOXO1 ENSG00000255513 RPL3L MSRB1 GFER TBL3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around GFER on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GFER gene promoter:

Genomic Locations for GFER Gene

Genomic Locations for GFER Gene
chr16:1,984,149-1,987,749
(GRCh38/hg38)
Size:
3,601 bases
Orientation:
Plus strand
chr16:2,034,150-2,037,750
(GRCh37/hg19)

Genomic View for GFER Gene

Genes around GFER on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GFER Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GFER Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GFER Gene

Proteins for GFER Gene

  • Protein details for GFER Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P55789-ALR_HUMAN
    Recommended name:
    FAD-linked sulfhydryl oxidase ALR
    Protein Accession:
    P55789
    Secondary Accessions:
    • Q53YM6
    • Q8TAH6
    • Q9H290
    • Q9UK40

    Protein attributes for GFER Gene

    Size:
    205 amino acids
    Molecular mass:
    23449 Da
    Cofactor:
    Name=FAD; Xref=ChEBI:CHEBI:57692;
    Quaternary structure:
    • Homodimer; disulfide-linked. May form heterodimers of isoform 1 and isoform 2.
    SequenceCaution:
    • Sequence=AAA96390.2; Type=Frameshift; Positions=70; Evidence={ECO:0000305}; Sequence=AAD36986.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAD56538.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH02429.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH28348.2; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for GFER Gene

    Alternative splice isoforms for GFER Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GFER Gene

Post-translational modifications for GFER Gene

Other Protein References for GFER Gene

No data available for DME Specific Peptides for GFER Gene

Domains & Families for GFER Gene

Gene Families for GFER Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for GFER Gene

Suggested Antigen Peptide Sequences for GFER Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with GFER: view

No data available for UniProtKB/Swiss-Prot for GFER Gene

Function for GFER Gene

Molecular function for GFER Gene

GENATLAS Biochemistry:
growth factor homolog of yeast ERV1 gene,15.1kDa, (?involved in oxidative phosphorylation),identical to SazB/C locus (see D16S530E)
UniProtKB/Swiss-Prot CatalyticActivity:
2 RC(R)SH + O(2) = RC(R)S-S(R)CR + H(2)O(2).
UniProtKB/Swiss-Prot Function:
Isoform 1: FAD-dependent sulfhydryl oxidase that regenerates the redox-active disulfide bonds in CHCHD4/MIA40, a chaperone essential for disulfide bond formation and protein folding in the mitochondrial intermembrane space. The reduced form of CHCHD4/MIA40 forms a transient intermolecular disulfide bridge with GFER/ERV1, resulting in regeneration of the essential disulfide bonds in CHCHD4/MIA40, while GFER/ERV1 becomes re-oxidized by donating electrons to cytochrome c or molecular oxygen.
UniProtKB/Swiss-Prot Function:
Isoform 2: May act as an autocrine hepatotrophic growth factor promoting liver regeneration.

Enzyme Numbers (IUBMB) for GFER Gene

Gene Ontology (GO) - Molecular Function for GFER Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12681488
GO:0008083 growth factor activity IEA --
GO:0015035 protein disulfide oxidoreductase activity IDA 22224850
GO:0016491 oxidoreductase activity IEA --
GO:0016971 flavin-linked sulfhydryl oxidase activity IBA --
genes like me logo Genes that share ontologies with GFER: view
genes like me logo Genes that share phenotypes with GFER: view

Human Phenotype Ontology for GFER Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for GFER Gene

MGI Knock Outs for GFER:

Clone Products

No data available for Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for GFER Gene

Localization for GFER Gene

Subcellular locations from UniProtKB/Swiss-Prot for GFER Gene

Isoform 1: Mitochondrion intermembrane space.
Isoform 2: Cytoplasm. Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GFER gene
Compartment Confidence
extracellular 5
mitochondrion 5
cytosol 5
nucleus 2
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
  • Mitochondria (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GFER Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IDA --
GO:0005758 mitochondrial intermembrane space IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with GFER: view

Pathways & Interactions for GFER Gene

genes like me logo Genes that share pathways with GFER: view

Gene Ontology (GO) - Biological Process for GFER Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001889 liver development IBA --
GO:0010469 regulation of receptor activity IEA --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with GFER: view

No data available for SIGNOR curated interactions for GFER Gene

Drugs & Compounds for GFER Gene

(4) Drugs for GFER Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
FAD Approved Pharma Target 0
Hydrogen peroxide Approved, Vet_approved Pharma 73
Oxygen Approved, Vet_approved Pharma 0
genes like me logo Genes that share compounds with GFER: view

Transcripts for GFER Gene

Unigene Clusters for GFER Gene

Growth factor, augmenter of liver regeneration:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GFER Gene

No ASD Table

Relevant External Links for GFER Gene

GeneLoc Exon Structure for
GFER
ECgene alternative splicing isoforms for
GFER

Expression for GFER Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GFER Gene

Protein differential expression in normal tissues from HIPED for GFER Gene

This gene is overexpressed in Adrenal (34.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for GFER Gene



Protein tissue co-expression partners for GFER Gene

NURSA nuclear receptor signaling pathways regulating expression of GFER Gene:

GFER

SOURCE GeneReport for Unigene cluster for GFER Gene:

Hs.27184

mRNA Expression by UniProt/SwissProt for GFER Gene:

P55789-ALR_HUMAN
Tissue specificity: Ubiquitously expressed. Highest expression in the testis and liver and low expression in the muscle.

Evidence on tissue expression from TISSUES for GFER Gene

  • Liver(4.6)
  • Kidney(4.4)
  • Skin(4.1)
  • Nervous system(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for GFER Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
Regions:
Head and neck:
  • eye
  • head
genes like me logo Genes that share expression patterns with GFER: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for GFER Gene

Orthologs for GFER Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for GFER Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GFER 34
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia GFER 33 34
  • 88.34 (n)
cow
(Bos Taurus)
Mammalia GFER 33 34
  • 86.93 (n)
mouse
(Mus musculus)
Mammalia Gfer 33 16 34
  • 81.56 (n)
rat
(Rattus norvegicus)
Mammalia Gfer 33
  • 80.54 (n)
oppossum
(Monodelphis domestica)
Mammalia GFER 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves GFER 33 34
  • 63.92 (n)
lizard
(Anolis carolinensis)
Reptilia GFER 34
  • 53 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gfer 33
  • 69.27 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.11036 33
zebrafish
(Danio rerio)
Actinopterygii gfer 33 34
  • 62.24 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG12534 35
  • 52 (a)
Alr 34
  • 29 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea F56C11.3 35 33 34
  • 52.55 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ERV1 34
  • 32 (a)
OneToOne
Species where no ortholog for GFER was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for GFER Gene

ENSEMBL:
Gene Tree for GFER (if available)
TreeFam:
Gene Tree for GFER (if available)

Paralogs for GFER Gene

(1) SIMAP similar genes for GFER Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with GFER: view

No data available for Paralogs for GFER Gene

Variants for GFER Gene

Sequence variations from dbSNP and Humsavar for GFER Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs121908192 pathogenic, Myopathy, mitochondrial progressive, with congenital cataract, hearing loss, and developmental delay, not provided, Myopathy, mitochondrial progressive, with congenital cataract, hearing loss and developmental delay (MPMCHD) [MIM:613076] 1,985,991(+) G/A coding_sequence_variant, missense_variant
rs370475970 pathogenic, Mitochondrial diseases 1,985,996(+) C/T coding_sequence_variant, missense_variant
rs863224028 likely-pathogenic, pathogenic, not provided, Mitochondrial diseases 1,984,415(+) CCC/CC coding_sequence_variant, frameshift
rs771809901 pathogenic, not provided 1,984,861(+) C/T coding_sequence_variant, stop_gained
rs147568500 likely-pathogenic, not provided 1,986,002(+) G/A/T coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for GFER Gene

Variant ID Type Subtype PubMed ID
nsv952901 CNV deletion 24416366
nsv571179 CNV loss 21841781
nsv523037 CNV loss 19592680
nsv521569 CNV loss 19592680
nsv471072 CNV loss 18288195
nsv471070 CNV gain 18288195
nsv1160329 CNV deletion 26073780
esv2422427 CNV duplication 17116639
dgv4859n54 CNV loss 21841781
dgv4858n54 CNV loss 21841781
dgv336n27 CNV loss 19166990

Variation tolerance for GFER Gene

Residual Variation Intolerance Score: 79.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.67; 45.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GFER Gene

Human Gene Mutation Database (HGMD)
GFER
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GFER

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GFER Gene

Disorders for GFER Gene

MalaCards: The human disease database

(11) MalaCards diseases for GFER Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
myopathy, mitochondrial progressive, with congenital cataract, hearing loss, and developmental delay
  • myopathy with cataract and combined respiratory chain deficiency
mitochondrial metabolism disease
  • mitochondrial diseases
mitochondrial disorders
  • mitochondrial encephalomyopathies
nodular regenerative hyperplasia
  • miliary hepatocellular adenomatosis
spinal canal and spinal cord meningioma
- elite association - COSMIC cancer census association via MalaCards
Search GFER in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

ALR_HUMAN
  • Myopathy, mitochondrial progressive, with congenital cataract, hearing loss and developmental delay (MPMCHD) [MIM:613076]: A disease characterized by progressive myopathy and partial combined respiratory-chain deficiency, congenital cataract, sensorineural hearing loss, and developmental delay. {ECO:0000269 PubMed:19409522, ECO:0000269 PubMed:20593814}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for GFER

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with GFER: view

No data available for Genatlas for GFER Gene

Publications for GFER Gene

  1. The mitochondrial disulfide relay system protein GFER is mutated in autosomal-recessive myopathy with cataract and combined respiratory-chain deficiency. (PMID: 19409522) Di Fonzo A … Comi GP (American journal of human genetics 2009) 3 4 22 58
  2. Identification of hepatopoietin dimerization, its interacting regions and alternative splicing of its transcription. (PMID: 12180965) Li Y … He F (European journal of biochemistry 2002) 3 4 22 58
  3. A new human gene located in the PKD1 region of chromosome 16 is a functional homologue to ERV1 of yeast. (PMID: 8575761) Lisowsky T … Schneider MC (Genomics 1995) 2 3 4 58
  4. An electron-transfer path through an extended disulfide relay system: the case of the redox protein ALR. (PMID: 22224850) Banci L … Tokatlidis K (Journal of the American Chemical Society 2012) 3 4 58
  5. Molecular recognition and substrate mimicry drive the electron-transfer process between MIA40 and ALR. (PMID: 21383138) Banci L … Tokatlidis K (Proceedings of the National Academy of Sciences of the United States of America 2011) 3 4 58

Products for GFER Gene

Sources for GFER Gene

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