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Aliases for RETREG1 Gene

Aliases for RETREG1 Gene

  • Reticulophagy Regulator 1 2 3 3 5
  • Family With Sequence Similarity 134 Member B 2 3
  • Reticulophagy Receptor 1 3 4
  • FAM134B 3 4
  • JK1 3 4
  • Family With Sequence Similarity 134, Member B 2
  • Reticulophagy Receptor FAM134B 3
  • Protein FAM134B 3
  • JK-1 3

External Ids for RETREG1 Gene

Previous HGNC Symbols for RETREG1 Gene

  • FAM134B

Summaries for RETREG1 Gene

Entrez Gene Summary for RETREG1 Gene

  • The protein encoded by this gene is a cis-Golgi transmembrane protein that may be necessary for the long-term survival of nociceptive and autonomic ganglion neurons. Mutations in this gene are a cause of hereditary sensory and autonomic neuropathy type IIB (HSAN IIB), and this gene may also play a role in susceptibility to vascular dementia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

GeneCards Summary for RETREG1 Gene

RETREG1 (Reticulophagy Regulator 1) is a Protein Coding gene. Diseases associated with RETREG1 include Neuropathy, Hereditary Sensory And Autonomic, Type Iib and Neuropathy, Hereditary Sensory And Autonomic, Type Iia. An important paralog of this gene is RETREG3.

UniProtKB/Swiss-Prot for RETREG1 Gene

  • Endoplasmic reticulum-anchored autophagy receptor that mediates ER delivery into lysosomes through sequestration into autophagosomes (PubMed:26040720). Promotes membrane remodeling and ER scission via its membrane bending capacity and targets the fragments into autophagosomes via interaction with ATG8 family proteins (PubMed:26040720). Required for long-term survival of nociceptive and autonomic ganglion neurons (PubMed:19838196, PubMed:26040720).

Additional gene information for RETREG1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RETREG1 Gene

Genomics for RETREG1 Gene

GeneHancer (GH) Regulatory Elements for RETREG1 Gene

Promoters and enhancers for RETREG1 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
GH05J016615 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 658.2 -0.3 -251 2.7 FOXA2 ZNF473 MZF1 SIN3A RFX5 YY1 ZEB1 ZNF335 GLIS2 ZNF366 RETREG1 LOC101929524 ENSG00000250415 ENSG00000201370 GC05M016623
GH05J016505 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 666.3 +108.8 108781 4.6 FOXA2 KLF17 RAD21 RFX5 YY1 ZNF335 EGR1 RCOR1 ELK4 SMARCC1 RETREG1 ZNF622 LOC101929524
GH05J016537 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 24.7 +77.7 77673 4 FOXA2 RAD21 RFX5 YY1 EGR1 RCOR1 FOS RXRA CEBPB REST RETREG1 ZNF622 ENSG00000250415 LOC101929524
GH05J016563 Enhancer 0.7 dbSUPER 23.2 +48.5 48497 9.7 PKNOX1 NFIB ZIC2 ZNF121 CTBP1 GATA3 POLR2A SCRT2 RCOR1 FOS RETREG1 ENSG00000250415 ZNF622 LOC101929524
GH05J016519 Enhancer 1 ENCODE dbSUPER 15.4 +95.8 95824 4 HDAC1 MEIS2 SOX13 PKNOX1 FOXA2 TAF1 TEAD4 TAL1 MAX CEBPG RETREG1 ZNF622 LOC101929524
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RETREG1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for RETREG1 Gene

Genomic Locations for RETREG1 Gene
chr5:16,472,816-16,617,058
(GRCh38/hg38)
Size:
144,243 bases
Orientation:
Minus strand
chr5:16,473,147-16,617,167
(GRCh37/hg19)
Size:
144,021 bases
Orientation:
Minus strand

Genomic View for RETREG1 Gene

Genes around RETREG1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RETREG1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RETREG1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RETREG1 Gene

Proteins for RETREG1 Gene

  • Protein details for RETREG1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H6L5-RETR1_HUMAN
    Recommended name:
    Reticulophagy regulator 1
    Protein Accession:
    Q9H6L5
    Secondary Accessions:
    • Q69YN8
    • Q9H6K6
    • Q9H764
    • Q9NXM8

    Protein attributes for RETREG1 Gene

    Size:
    497 amino acids
    Molecular mass:
    54681 Da
    Quaternary structure:
    • Interacts with ATG8 family modifier proteins MAP1LC3A, MAP1LC3B, GABARAP, GABARAPL1 and GABARAPL2.
    SequenceCaution:
    • Sequence=AAH30517.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA90982.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB15252.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for RETREG1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RETREG1 Gene

Post-translational modifications for RETREG1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RETREG1 Gene

Domains & Families for RETREG1 Gene

Gene Families for RETREG1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted membrane proteins

Protein Domains for RETREG1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RETREG1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H6L5

UniProtKB/Swiss-Prot:

RETR1_HUMAN :
  • The LIR motif interacts with ATG8 family proteins and is necessary to target the ER fragments to autophagosomes for subsequent lysosomal degradation.
  • Belongs to the RETREG family.
Domain:
  • The LIR motif interacts with ATG8 family proteins and is necessary to target the ER fragments to autophagosomes for subsequent lysosomal degradation.
  • The reticulon homology domain provides capacity to bend the membrane and promotes ER scission (PubMed:26040720). This domain does not show relevant similarities with reticulon domains, preventing any domain predictions within the protein sequence.
Family:
  • Belongs to the RETREG family.
genes like me logo Genes that share domains with RETREG1: view

Function for RETREG1 Gene

Molecular function for RETREG1 Gene

UniProtKB/Swiss-Prot Function:
Endoplasmic reticulum-anchored autophagy receptor that mediates ER delivery into lysosomes through sequestration into autophagosomes (PubMed:26040720). Promotes membrane remodeling and ER scission via its membrane bending capacity and targets the fragments into autophagosomes via interaction with ATG8 family proteins (PubMed:26040720). Required for long-term survival of nociceptive and autonomic ganglion neurons (PubMed:19838196, PubMed:26040720).

Phenotypes From GWAS Catalog for RETREG1 Gene

Gene Ontology (GO) - Molecular Function for RETREG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 26040720
genes like me logo Genes that share ontologies with RETREG1: view
genes like me logo Genes that share phenotypes with RETREG1: view

Human Phenotype Ontology for RETREG1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for RETREG1 Gene

MGI Knock Outs for RETREG1:

Animal Model Products

miRNA for RETREG1 Gene

miRTarBase miRNAs that target RETREG1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for RETREG1 Gene

Localization for RETREG1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RETREG1 Gene

Golgi apparatus, cis-Golgi network membrane; Multi-pass membrane protein. Endoplasmic reticulum membrane; Multi-pass membrane protein.

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 RETREG1 gene
Compartment Confidence
nucleus 5
endoplasmic reticulum 5
plasma membrane 3
golgi apparatus 3
peroxisome 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RETREG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005730 nucleolus IDA --
GO:0005783 endoplasmic reticulum IDA,IEA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005794 Golgi apparatus IEA --
GO:0005801 cis-Golgi network IEA,ISS --
genes like me logo Genes that share ontologies with RETREG1: view

Pathways & Interactions for RETREG1 Gene

SuperPathways for RETREG1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RETREG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006914 autophagy IEA --
GO:0019233 sensory perception of pain IMP 19838196
GO:0043524 negative regulation of neuron apoptotic process IEA,IMP 26040720
GO:0061709 reticulophagy IMP 26040720
genes like me logo Genes that share ontologies with RETREG1: view

No data available for Pathways by source and SIGNOR curated interactions for RETREG1 Gene

Drugs & Compounds for RETREG1 Gene

No Compound Related Data Available

Transcripts for RETREG1 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RETREG1 Gene

No ASD Table

Relevant External Links for RETREG1 Gene

GeneLoc Exon Structure for
RETREG1
ECgene alternative splicing isoforms for
RETREG1

Expression for RETREG1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of RETREG1 Gene:

RETREG1

mRNA Expression by UniProt/SwissProt for RETREG1 Gene:

Q9H6L5-RETR1_HUMAN
Tissue specificity: Overexpressed in esophageal squamous cell carcinoma (PubMed:17487424).

Evidence on tissue expression from TISSUES for RETREG1 Gene

  • Intestine(4.3)
  • Lung(4.2)
  • Nervous system(3.8)
  • Kidney(2.6)
  • Muscle(2.3)
  • Heart(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RETREG1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • olfactory bulb
  • skull
  • tongue
Thorax:
  • chest wall
  • clavicle
  • esophagus
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • stomach
Pelvis:
  • pelvis
  • prostate
  • urinary bladder
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood vessel
  • bone marrow
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • sweat gland
  • vertebrae
genes like me logo Genes that share expression patterns with RETREG1: view

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for RETREG1 Gene

Orthologs for RETREG1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RETREG1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia FAM134B 34 33
  • 99.66 (n)
OneToOne
dog
(Canis familiaris)
Mammalia FAM134B 34 33
  • 91.52 (n)
OneToOne
cow
(Bos Taurus)
Mammalia FAM134B 34 33
  • 90.17 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Fam134b 33
  • 87.92 (n)
mouse
(Mus musculus)
Mammalia Fam134b 34 33
  • 86.39 (n)
OneToOne
Retreg1 16
platypus
(Ornithorhynchus anatinus)
Mammalia FAM134B 34
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia FAM134B 34
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC100859798 33
  • 75.8 (n)
FAM134B 34
  • 58 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia FAM134B 34
  • 60 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia fam134b 33
  • 66.67 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100003524 33
  • 57.61 (n)
BX323064.1 34
  • 41 (a)
OneToOne
Species where no ortholog for RETREG1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for RETREG1 Gene

ENSEMBL:
Gene Tree for RETREG1 (if available)
TreeFam:
Gene Tree for RETREG1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RETREG1: view image

Paralogs for RETREG1 Gene

Paralogs for RETREG1 Gene

genes like me logo Genes that share paralogs with RETREG1: view

Variants for RETREG1 Gene

Sequence variations from dbSNP and Humsavar for RETREG1 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs137852736 pathogenic, Hereditary sensory and autonomic neuropathy type IIA 16,616,953(-) GAG/G coding_sequence_variant, frameshift, genic_upstream_transcript_variant
rs137852737 pathogenic, Hereditary sensory and autonomic neuropathy type IIB, Hereditary sensory and autonomic neuropathy type IIA 16,565,788(-) G/A coding_sequence_variant, genic_upstream_transcript_variant, stop_gained
rs137852738 pathogenic, Hereditary sensory and autonomic neuropathy type IIA 16,478,032(-) A/G splice_donor_variant
rs137852739 pathogenic, Hereditary sensory and autonomic neuropathy type IIB, Hereditary sensory and autonomic neuropathy type IIA, not provided 16,477,736(-) G/A/C coding_sequence_variant, missense_variant, stop_gained
rs143878016 likely-benign, uncertain-significance, not specified, Hereditary sensory and autonomic neuropathy type II, Hereditary sensory and autonomic neuropathy type IIB 16,481,072(-) C/T coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for RETREG1 Gene

Variant ID Type Subtype PubMed ID
dgv935e201 CNV deletion 23290073
esv1003044 CNV insertion 20482838
esv1371607 CNV insertion 17803354
esv1983383 CNV deletion 18987734
esv2664300 CNV deletion 23128226
esv2670384 CNV deletion 23128226
esv2729832 CNV deletion 23290073
esv2729834 CNV deletion 23290073
esv2729835 CNV deletion 23290073
esv2729836 CNV deletion 23290073
esv275370 CNV loss 21479260
esv3565578 CNV deletion 23714750
esv3604132 CNV gain 21293372
esv3604133 CNV loss 21293372
esv3604134 CNV loss 21293372
nsv1073442 CNV deletion 25765185
nsv1073443 CNV deletion 25765185
nsv1114653 CNV deletion 24896259
nsv1114654 CNV deletion 24896259
nsv1142630 CNV deletion 24896259
nsv1144103 CNV deletion 24896259
nsv1152313 CNV insertion 26484159
nsv476191 CNV novel sequence insertion 20440878

Variation tolerance for RETREG1 Gene

Residual Variation Intolerance Score: 40.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.15; 51.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RETREG1 Gene

Human Gene Mutation Database (HGMD)
RETREG1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RETREG1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RETREG1 Gene

Disorders for RETREG1 Gene

MalaCards: The human disease database

(9) MalaCards diseases for RETREG1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

RETR1_HUMAN
  • Neuropathy, hereditary sensory and autonomic, 2B (HSAN2B) [MIM:613115]: A form of hereditary sensory and autonomic neuropathy, a genetically and clinically heterogeneous group of disorders characterized by degeneration of dorsal root and autonomic ganglion cells, and by sensory and/or autonomic abnormalities. HSAN2B is an autosomal recessive disorder characterized by impairment of pain, temperature and touch sensation. Onset occurs in the first or second decade, with impaired nociception and progressive mutilating ulceration of the hands and feet with osteomyelitis and acroosteolysis. Amputations of the hands and feet are common. Autonomic dysfunction includes hyperhidrosis, urinary incontinence, and slow pupillary light response. {ECO:0000269 PubMed:19838196}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for RETREG1

genes like me logo Genes that share disorders with RETREG1: view

No data available for Genatlas for RETREG1 Gene

Publications for RETREG1 Gene

  1. Mutations in FAM134B, encoding a newly identified Golgi protein, cause severe sensory and autonomic neuropathy. (PMID: 19838196) Kurth I … Hübner CA (Nature genetics 2009) 2 3 4 58
  2. Regulation of endoplasmic reticulum turnover by selective autophagy. (PMID: 26040720) Khaminets A … Dikic I (Nature 2015) 3 4 58
  3. Mutation in FAM134B causing hereditary sensory neuropathy with spasticity in a Turkish family. (PMID: 24327336) Ilgaz Aydinlar E … Parman Y (Muscle & nerve 2014) 2 3 58
  4. Oncogenic properties of a novel gene JK-1 located in chromosome 5p and its overexpression in human esophageal squamous cell carcinoma. (PMID: 17487424) Tang WK … Tang JC (International journal of molecular medicine 2007) 3 4 58
  5. Novel FAM134B mutations and their clinicopathological significance in colorectal cancer. (PMID: 28144752) Islam F … Lam AK (Human genetics 2017) 3 58

Products for RETREG1 Gene

Sources for RETREG1 Gene

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