GPM6B Gene (Protein Coding)

Glycoprotein M6B

GC0XM013789
GIFtS:
37
This gene encodes a membrane glycoprotein that belongs to the proteolipid protein family. Proteolipid protein family members are expressed in most brain regions and are thought to be involved in cellular housekeeping functions such as membrane trafficking and cell-to-cell communication. This protein may also be involved in osteoblast differentiation. Alternate splicing results ... See more...

Aliases for GPM6B Gene

Aliases for GPM6B Gene

  • Glycoprotein M6B 2 3 5
  • M6B 2 3 4
  • Neuronal Membrane Glycoprotein M6-B 3 4
  • Protolipid M6B 3
  • MGC17150 2
  • MGC54284 2
  • GPM6B 5
  • M6b 4

External Ids for GPM6B Gene

Previous GeneCards Identifiers for GPM6B Gene

  • GC0XM013030
  • GC0XM012608
  • GC0XM013150
  • GC0XM013548
  • GC0XM013698
  • GC0XM011546

Summaries for GPM6B Gene

Entrez Gene Summary for GPM6B Gene

  • This gene encodes a membrane glycoprotein that belongs to the proteolipid protein family. Proteolipid protein family members are expressed in most brain regions and are thought to be involved in cellular housekeeping functions such as membrane trafficking and cell-to-cell communication. This protein may also be involved in osteoblast differentiation. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are located on chromosomes Y and 22. [provided by RefSeq, Jan 2016]

GeneCards Summary for GPM6B Gene

GPM6B (Glycoprotein M6B) is a Protein Coding gene. Diseases associated with GPM6B include Pelizaeus-Merzbacher Disease and Neuronal Ceroid Lipofuscinosis. An important paralog of this gene is GPM6A.

UniProtKB/Swiss-Prot Summary for GPM6B Gene

  • May be involved in neural development. Involved in regulation of osteoblast function and bone formation. Involved in matrix vesicle release by osteoblasts; this function seems to involve maintenance of the actin cytoskeleton. May be involved in cellular trafficking of SERT and thereby in regulation of serotonin uptake.

Gene Wiki entry for GPM6B Gene

Additional gene information for GPM6B Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GPM6B Gene

Genomics for GPM6B Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for GPM6B 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
GH0XJ013936 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +0.8 755 4.5 RNF2 CEBPG PRDM10 ZNF692 LARP7 PRDM1 ZIC2 PATZ1 ZNF600 ZNF341 GPM6B GEMIN8 RF00017-8167 RF00017-8165 OFD1
GH0XJ013817 Promoter/Enhancer 1.1 EPDnew Ensembl dbSUPER 600.1 +123.2 123223 4 RNF2 POLR2A USF1 SMARCA4 CBX8 GPM6B TRAPPC2 RF00017-8166 AB372778-029 RF00017-8165 OFD1
GH0XJ013897 Enhancer 1.1 Ensembl ENCODE dbSUPER 41.3 +39.4 39433 3.2 CTCF ATF7 PRDM10 ZNF629 RAD21 TRIM22 ZNF600 YY1 ZNF341 SCRT2 hsa-miR-5096-185 lnc-GEMIN8-2 GPM6B RF00017-8167 RF00017-8165 OFD1
GH0XJ013893 Enhancer 0.5 Ensembl dbSUPER 28.6 +44.8 44823 1.2 ZIC2 GLIS1 GPM6B lnc-GEMIN8-2 lnc-OFD1-2 RF00017-8165 OFD1
GH0XJ013905 Enhancer 0.6 Ensembl ENCODE dbSUPER 22.3 +32.7 32724 2.2 PRDM4 RF00017-8167 GPM6B hsa-miR-5096-185 RF00017-8165 OFD1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GPM6B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for GPM6B

Top Transcription factor binding sites by QIAGEN in the GPM6B gene promoter:
  • FOXO4
  • GATA-3
  • GR
  • GR-alpha
  • GR-beta
  • PPAR-gamma1
  • PPAR-gamma2
  • Roaz
  • RSRFC4
  • S8

Genomic Locations for GPM6B Gene

Genomic Locations for GPM6B Gene
chrX:13,770,922-13,938,824
(GRCh38/hg38)
Size:
167,903 bases
Orientation:
Minus strand
chrX:13,789,062-13,956,831
(GRCh37/hg19)
Size:
167,770 bases
Orientation:
Minus strand

Genomic View for GPM6B Gene

Genes around GPM6B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GPM6B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GPM6B Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for GPM6B Gene

Proteins for GPM6B Gene

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  • Protein details for GPM6B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13491-GPM6B_HUMAN
    Recommended name:
    Neuronal membrane glycoprotein M6-b
    Protein Accession:
    Q13491
    Secondary Accessions:
    • O76077
    • Q86X43
    • Q8N956

    Protein attributes for GPM6B Gene

    Size:
    265 amino acids
    Molecular mass:
    28989 Da
    Quaternary structure:
    • Interacts with SERT.
    SequenceCaution:
    • Sequence=AAB16888.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAC19165.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for GPM6B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GPM6B Gene

Protein Expression for GPM6B Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for GPM6B Gene

  • Glycosylation at Asn73 and Asn177
  • Modification sites at PhosphoSitePlus

Other Protein References for GPM6B Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for GPM6B Gene

Domains & Families for GPM6B Gene

Gene Families for GPM6B Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for GPM6B Gene

InterPro:
Blocks:
  • Myelin proteolipid protein (PLP)
ProtoNet:

Suggested Antigen Peptide Sequences for GPM6B Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ59871, highly similar to Neuronal membrane glycoprotein M6-b (B7Z248_HUMAN)
  • cDNA FLJ54144, highly similar to Neuronal membrane glycoprotein M6-b (B7Z613_HUMAN)
  • Neuronal membrane glycoprotein M6-b (GPM6B_HUMAN)
  • cDNA FLJ38338 fis, clone FCBBF3027104, highly similar to Mus musculus proteolipid M6B isoform alpha-beta-TMD-omega (M6B) mRNA (Q8N956_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q13491

UniProtKB/Swiss-Prot:

GPM6B_HUMAN :
  • Belongs to the myelin proteolipid protein family.
Family:
  • Belongs to the myelin proteolipid protein family.
genes like me logo Genes that share domains with GPM6B: view

Function for GPM6B Gene

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Molecular function for GPM6B Gene

UniProtKB/Swiss-Prot Function:
May be involved in neural development. Involved in regulation of osteoblast function and bone formation. Involved in matrix vesicle release by osteoblasts; this function seems to involve maintenance of the actin cytoskeleton. May be involved in cellular trafficking of SERT and thereby in regulation of serotonin uptake.
GENATLAS Biochemistry:
neuronal membrane glycoprotein M6B,with strong homology to PLP, murine Gpm6 homolog

Phenotypes From GWAS Catalog for GPM6B Gene

Gene Ontology (GO) - Molecular Function for GPM6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with GPM6B: view
genes like me logo Genes that share phenotypes with GPM6B: view

Animal Models for GPM6B Gene

MGI Knock Outs for GPM6B:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for GPM6B Gene

Localization for GPM6B Gene

Subcellular locations from UniProtKB/Swiss-Prot for GPM6B Gene

Cell membrane. Multi-pass membrane protein. Note=Colocalizes with SERT at the plasma membrane. {ECO:0000250}.

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 GPM6B gene
Compartment Confidence
plasma membrane 5
peroxisome 2
extracellular 1
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for GPM6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IBA,ISS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0045121 membrane raft IBA,ISS --
genes like me logo Genes that share ontologies with GPM6B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for GPM6B Gene

Pathways & Interactions for GPM6B Gene

PathCards logo

SuperPathways for GPM6B Gene

No Data Available

Gene Ontology (GO) - Biological Process for GPM6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001503 ossification IEA --
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development NAS 8661015
GO:0015031 protein transport IEA --
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with GPM6B: view

No data available for Pathways by source and SIGNOR curated interactions for GPM6B Gene

Drugs & Compounds for GPM6B Gene

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  1. Drug
No Compound Related Data Available

Transcripts for GPM6B Gene

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  2. miRNA
  3. Inhibitory RNA
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mRNA/cDNA for GPM6B Gene

5 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GPM6B

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GPM6B Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c · 9d · 9e ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b · 13c · 13d ^ 14 ^ 15 ^ 16 ^
SP1: -
SP2:
SP3: - -
SP4: -
SP5: - - - - - - - - - - - - -
SP6: - - - - - - - - - - - - - -
SP7: - - - - - - - - - - - -
SP8: - - - - - - - - -
SP9: - - - - - - - - - - - -
SP10: - - - - - - - - - - - -
SP11: -
SP12: - - - - - - - -
SP13:

ExUns: 17a · 17b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for GPM6B Gene

GeneLoc Exon Structure for
GPM6B

Expression for GPM6B Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GPM6B Gene

mRNA expression in normal human tissues for GPM6B Gene
mRNA expression by GTEx for GPM6B GenemRNA expression by BioGPS for GPM6B Gene

mRNA differential expression in normal tissues according to GTEx for GPM6B Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x7.6), Brain - Amygdala (x5.1), Brain - Hippocampus (x4.8), Brain - Substantia nigra (x4.4), and Brain - Caudate (basal ganglia) (x4.0).

Protein differential expression in normal tissues from HIPED for GPM6B Gene

This gene is overexpressed in Frontal cortex (43.6), Spinal cord (8.1), and Retina (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for GPM6B Gene



Protein tissue co-expression partners for GPM6B Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for GPM6B

SOURCE GeneReport for Unigene cluster for GPM6B Gene:

Hs.495710

mRNA Expression by UniProt/SwissProt for GPM6B Gene:

Q13491-GPM6B_HUMAN
Tissue specificity: Neurons and glia; cerebellar Bergmann glia, in glia within white matter tracts of the cerebellum and cerebrum, and in embryonic dorsal root ganglia.

Evidence on tissue expression from TISSUES for GPM6B Gene

  • Nervous system(5)
  • Eye(2.5)
  • Skin(2.2)
  • Blood(2)
genes like me logo Genes that share expression patterns with GPM6B: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for GPM6B Gene

Orthologs for GPM6B Gene

This gene was present in the common ancestor of animals.

Orthologs for GPM6B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia GPM6B 30 31
  • 100 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Gpm6b 30 17 31
  • 93.7 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia GPM6B 30 31
  • 93.39 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia GPM6B 31
  • 92 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia GPM6B 31
  • 88 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia GPM6B 31
  • 79 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves GPM6B 30 31
  • 84.95 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia GPM6B 31
  • 92 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia gpm6b 30
  • 82.64 (n)
Str.2894 30
African clawed frog
(Xenopus laevis)
 Amphibia Xl.14003 30
Zebrafish
(Danio rerio)
 Actinopterygii gpm6bb 31
  • 68 (a)
 OneToOne
Dr.28505 30
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.10467 30
Fruit Fly
(Drosophila melanogaster)
 Insecta M6 31
  • 24 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 39 (a)
 OneToMany
Species where no ortholog for GPM6B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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 GPM6B Gene

ENSEMBL:
Gene Tree for GPM6B (if available)
TreeFam:
Gene Tree for GPM6B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GPM6B: view image

Paralogs for GPM6B Gene

Paralogs for GPM6B Gene

(3) SIMAP similar genes for GPM6B Gene using alignment to 8 proteins:

  • GPM6B_HUMAN
  • B7Z248_HUMAN
  • B7Z613_HUMAN
  • C9J028_HUMAN
  • C9J8H8_HUMAN
  • C9JZE8_HUMAN
  • H7C5A8_HUMAN
  • H7C5H4_HUMAN

Pseudogenes.org Pseudogenes for GPM6B Gene

genes like me logo Genes that share paralogs with GPM6B: view

Variants for GPM6B Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GPM6B Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
778977 Benign: not provided 13,776,244(-) A/G SYNONYMOUS_VARIANT
rs1555910377 Likely Benign: not specified 13,777,346(-) G/A INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for GPM6B Gene

Structural Variations from Database of Genomic Variants (DGV) for GPM6B Gene

Variant ID Type Subtype PubMed ID
esv2661778 CNV deletion 23128226
esv3573596 CNV loss 25503493
esv991320 CNV deletion 20482838
nsv1075308 CNV deletion 25765185
nsv1142566 CNV tandem duplication 24896259
nsv1144317 CNV deletion 24896259
nsv472412 CNV novel sequence insertion 20440878
nsv473578 CNV novel sequence insertion 20440878
nsv510816 CNV deletion 20534489
nsv512670 CNV loss 21212237
nsv516360 CNV loss 19592680
nsv526098 CNV loss 19592680
nsv528634 CNV gain 19592680
nsv953403 CNV deletion 24416366

Variation tolerance for GPM6B Gene

Residual Variation Intolerance Score: 20.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.44; 9.65% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GPM6B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
GPM6B

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GPM6B Gene

Disorders for GPM6B Gene

MalaCards: The human disease database

(2) MalaCards diseases for GPM6B Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
pelizaeus-merzbacher disease
  • pmd
neuronal ceroid lipofuscinosis
  • batten disease
- elite association - COSMIC cancer census association via MalaCards
Search GPM6B in MalaCards View complete list of genes associated with diseases

Additional Disease Information for GPM6B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with GPM6B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for GPM6B Gene

Publications for GPM6B Gene

  1. Chromosomal mapping of the human M6 genes. (PMID: 8661015) Olinsky S … Narayanan V (Genomics 1996) 2 3 4 23
  2. GPM6B regulates osteoblast function and induction of mineralization by controlling cytoskeleton and matrix vesicle release. (PMID: 21638316) Drabek K … van Leeuwen JP (Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2011) 3 4
  3. Membrane glycoprotein M6B interacts with the human serotonin transporter. (PMID: 18581270) Fjorback AW … Wiborg O (Journal of molecular neuroscience : MN 2009) 3 4
  4. Fetal hemoglobin in sickle cell anemia: Bayesian modeling of genetic associations. (PMID: 17918249) Sebastiani P … Steinberg MH (American journal of hematology 2008) 3 41
  5. PLP1 and GPM6B intragenic copy number analysis by MAPH in 262 patients with hypomyelinating leukodystrophies: Identification of one partial triplication and two partial deletions of PLP1. (PMID: 16416265) Combes P … Vaurs-Barrière C (Neurogenetics 2006) 3 41

ExternalLinks

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