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GPM6A glycoprotein M6A [ Homo sapiens (human) ]

Gene ID: 2823, updated on 1-Jun-2020

Summary

Official Symbol
GPM6Aprovided by HGNC
Official Full Name
glycoprotein M6Aprovided by HGNC
Primary source
HGNC:HGNC:4460
See related
Ensembl:ENSG00000150625 MIM:601275
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
M6A; GPM6
Expression
Biased expression in brain (RPKM 247.1) and lung (RPKM 8.5) See more
Orthologs

Genomic context

See GPM6A in Genome Data Viewer
Location:
4q34.2
Exon count:
11
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (175632937..176002691, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (176554088..176923842, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene tRNA splicing endonuclease subunit 2 pseudogene 1 Neighboring gene ADAM metallopeptidase domain 20 pseudogene 2 Neighboring gene uncharacterized LOC101928590 Neighboring gene uncharacterized LOC107984113 Neighboring gene microtubule affinity regulating kinase 2 pseudogene 4 Neighboring gene WD repeat domain 17

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
NHGRI GWA Catalog
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
NHGRI GWA Catalog
Genome-wide association study of temperament in bipolar disorder reveals significant associations with three novel Loci.
NHGRI GWA Catalog
Genomic variation associated with mortality among adults of European and African ancestry with heart failure: the cohorts for heart and aging research in genomic epidemiology consortium.
NHGRI GWA Catalog
GWAS of 126,559 individuals identifies genetic variants associated with educational attainment.
NHGRI GWA Catalog
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef The yeast two-hybrid screen and the coimmunoprecipitation analysis identify the HIV-1 Nef interacting human protein glycoprotein M6A (GPM6A) in cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium channel activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
calcium ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
neural retina development ISS
Inferred from Sequence or Structural Similarity
more info
 
neuron migration IDA
Inferred from Direct Assay
more info
PubMed 
neuron projection development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuron projection morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of filopodium assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of synapse organization IEA
Inferred from Electronic Annotation
more info
 
response to bacterium IEA
Inferred from Electronic Annotation
more info
 
stem cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
axonal growth cone IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axonal growth cone ISS
Inferred from Sequence or Structural Similarity
more info
 
dendritic spine IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
extracellular vesicle HDA PubMed 
filopodium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
filopodium ISS
Inferred from Sequence or Structural Similarity
more info
 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
integral component of presynaptic active zone membrane IEA
Inferred from Electronic Annotation
more info
 
neuron projection ISS
Inferred from Sequence or Structural Similarity
more info
 
neuronal cell body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuronal cell body ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
neuronal membrane glycoprotein M6-a

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001261447.1NP_001248376.1  neuronal membrane glycoprotein M6-a isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks three consecutive internal exons and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AI609188, BC010461, DA507772, DA528125
    Conserved Domains (1) summary
    cl02417
    Location:94212
    Myelin_PLP; Myelin proteolipid protein (PLP or lipophilin)
  2. NM_001261448.1NP_001248377.1  neuronal membrane glycoprotein M6-a isoform 4

    See identical proteins and their annotated locations for NP_001248377.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (4) is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AI609188, AK299788, BC010461, DC353381
    Consensus CDS
    CCDS58936.1
    UniProtKB/Swiss-Prot
    P51674
    Related
    ENSP00000423984.1, ENST00000515090.5
    Conserved Domains (1) summary
    pfam01275
    Location:7240
    Myelin_PLP; Myelin proteolipid protein (PLP or lipophilin)
  3. NM_005277.4NP_005268.1  neuronal membrane glycoprotein M6-a isoform 1

    See identical proteins and their annotated locations for NP_005268.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform 1. Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AI609188, BC010461, DA507772, DA915764
    Consensus CDS
    CCDS3824.1
    UniProtKB/Swiss-Prot
    P51674
    Related
    ENSP00000280187.7, ENST00000280187.11
    Conserved Domains (1) summary
    pfam01275
    Location:14247
    Myelin_PLP; Myelin proteolipid protein (PLP or lipophilin)
  4. NM_201591.2NP_963885.1  neuronal membrane glycoprotein M6-a isoform 1

    See identical proteins and their annotated locations for NP_963885.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AI609188, BC010461, D49958, DA190376, DA196860
    Consensus CDS
    CCDS3824.1
    UniProtKB/Swiss-Prot
    P51674
    Related
    ENSP00000377268.2, ENST00000393658.6
    Conserved Domains (1) summary
    pfam01275
    Location:14247
    Myelin_PLP; Myelin proteolipid protein (PLP or lipophilin)
  5. NM_201592.2NP_963886.1  neuronal membrane glycoprotein M6-a isoform 3

    See identical proteins and their annotated locations for NP_963886.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an internal exon and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AI609188, AK226176, BC010461, DA507772
    Consensus CDS
    CCDS54822.1
    UniProtKB/Swiss-Prot
    P51674
    Related
    ENSP00000421578.1, ENST00000506894.5
    Conserved Domains (1) summary
    pfam01275
    Location:3236
    Myelin_PLP; Myelin proteolipid protein (PLP or lipophilin)

RNA

  1. NR_048571.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks two consecutive internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI609188, BC010461, DA507772, DA621566

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    175632937..176002691 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011531877.1XP_011530179.1  neuronal membrane glycoprotein M6-a isoform X1

    See identical proteins and their annotated locations for XP_011530179.1

    Conserved Domains (1) summary
    pfam01275
    Location:2184
    Myelin_PLP; Myelin proteolipid protein (PLP or lipophilin)
  2. XM_006714183.1XP_006714246.1  neuronal membrane glycoprotein M6-a isoform X1

    See identical proteins and their annotated locations for XP_006714246.1

    Conserved Domains (1) summary
    pfam01275
    Location:2184
    Myelin_PLP; Myelin proteolipid protein (PLP or lipophilin)
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