GPM6A glycoprotein M6A [Homo sapiens (human)] - Gene

Summary

Official Symbol: GPM6Aprovided by HGNC
Official Full Name: glycoprotein M6Aprovided by HGNC
Primary source: HGNC:HGNC:4460
See related: Ensembl:ENSG00000150625 MIM:601275; AllianceGenome:HGNC:4460
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
Summary: Predicted to enable calcium channel activity. Involved in neuron migration and stem cell differentiation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in brain (RPKM 247.1) and lung (RPKM 8.5) See more
Orthologs: mouse all
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Genomic context

Location:: 4q34.2

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (175632937..176002691, complement)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (178971366..179341143, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (176554088..176923842, complement)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

GPM6A expression is suppressed in hepatocellular carcinoma through miRNA-96 production.
Title: GPM6A expression is suppressed in hepatocellular carcinoma through miRNA-96 production.
Biological and pharmacological roles of m[6]A modifications in cancer drug resistance.
Title: Biological and pharmacological roles of m(6)A modifications in cancer drug resistance.
The Glycoprotein M6a Is Associated with Invasiveness and Radioresistance of Glioblastoma Stem Cells.
Title: The Glycoprotein M6a Is Associated with Invasiveness and Radioresistance of Glioblastoma Stem Cells.
CircCCNB1 silencing acting as a miR-106b-5p sponge inhibited GPM6A expression to promote HCC progression by enhancing DYNC1I1 expression and activating the AKT/ERK signaling pathway.
Title: CircCCNB1 silencing acting as a miR-106b-5p sponge inhibited GPM6A expression to promote HCC progression by enhancing DYNC1I1 expression and activating the AKT/ERK signaling pathway.
Physio-pathological effects of m6A modification and its potential contribution to melanoma.
Title: Physio-pathological effects of m6A modification and its potential contribution to melanoma.
NPM1 Is a Prognostic Biomarker Involved in Immune Infiltration of Lung Adenocarcinoma and Associated With m6A Modification and Glycolysis.
Title: NPM1 Is a Prognostic Biomarker Involved in Immune Infiltration of Lung Adenocarcinoma and Associated With m6A Modification and Glycolysis.
Screening and Identifying m6A Regulators as an Independent Prognostic Biomarker in Pancreatic Cancer Based on The Cancer Genome Atlas Database.
Title: Screening and Identifying m6A Regulators as an Independent Prognostic Biomarker in Pancreatic Cancer Based on The Cancer Genome Atlas Database.
A comprehensive study on identifying the structural and functional SNPs of human neuronal membrane glycoprotein M6A (GPM6A).
Title: A comprehensive study on identifying the structural and functional SNPs of human neuronal membrane glycoprotein M6A (GPM6A).
Multiomics integrative analysis for gene signatures and prognostic values of m(6)A regulators in pancreatic adenocarcinoma: a retrospective study in The Cancer Genome Atlas project.
Title: Multiomics integrative analysis for gene signatures and prognostic values of m(6)A regulators in pancreatic adenocarcinoma: a retrospective study in The Cancer Genome Atlas project.
Authors report on N6-methyladenosine (m6A) RNA modification profiles of human peripheral blood mononuclear cells (PBMCs) from young and old cohorts. An m6A RNA profile identified a decrease in overall RNA methylation during the aging process as well as the predominant modification on proteincoding mRNAs.
Title: Profiling of m6A RNA modifications identified an age-associated regulation of AGO2 mRNA stability.

Submit: New GeneRIF Correction See all GeneRIFs (21)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of temperament in bipolar disorder reveals significant associations with three novel Loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
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. EBI GWAS Catalog EBI GWAS CatalogPubMed
GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-83382 (e-PCR)
- UniSTS:101891

RH104009 (e-PCR)
- UniSTS:98334

D4S3030 (e-PCR), detects polymorphism
- UniSTS:13858

STS-R49342 (e-PCR)
- UniSTS:26680

RH48750 (e-PCR)
- UniSTS:842

SHGC-59781 (e-PCR)
- UniSTS:64381

D4S3028 (e-PCR)
- UniSTS:63105

SHGC-82659 (e-PCR)
- UniSTS:95621

RH123651 (e-PCR)
- UniSTS:136073

D4S2765E (e-PCR)
- UniSTS:153745

WI-21773 (e-PCR)
- UniSTS:8348

RH35844 (e-PCR)
- UniSTS:8349

SHGC-67744 (e-PCR)
- UniSTS:33696

SHGC-51395 (e-PCR)
- UniSTS:26319

RH119227 (e-PCR)
- UniSTS:138736

D4S450 (e-PCR)
- UniSTS:24319

Homology

Homologs of the GPM6A gene: The GPM6A gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, and frog.
Orthologs from Annotation Pipeline: 407 organisms have orthologs with human gene GPM6A
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium channel activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in calcium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in neural retina development	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron migration	IDA Inferred from Direct Assay more info	PubMed
involved_in neuron projection development	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in neuron projection morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of filopodium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of synapse organization	IEA Inferred from Electronic Annotation more info
involved_in response to bacterium	IEA Inferred from Electronic Annotation more info
involved_in stem cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in synapse assembly	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in axonal growth cone	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in axonal growth cone	ISS Inferred from Sequence or Structural Similarity more info
located_in dendritic spine	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular vesicle	HDA more info	PubMed
is_active_in filopodium	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in filopodium	ISS Inferred from Sequence or Structural Similarity more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in neuron projection	ISS Inferred from Sequence or Structural Similarity more info
is_active_in neuronal cell body	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in neuronal cell body	ISS Inferred from Sequence or Structural Similarity more info
located_in parallel fiber to Purkinje cell synapse	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in presynaptic active zone membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: neuronal membrane glycoprotein M6-a

NCBI Reference Sequences (RefSeq)

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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)

NM_001261447.1 → NP_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:94 → 212

Myelin_PLP; Myelin proteolipid protein (PLP or lipophilin)
NM_001261448.1 → NP_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:7 → 240

Myelin_PLP; Myelin proteolipid protein (PLP or lipophilin)
NM_001388090.1 → NP_001375019.1 neuronal membrane glycoprotein M6-a isoform 5

Status: VALIDATED

Description

Transcript Variant: Variants 7 and 8 encode the same isoform (5).

Source sequence(s)

AC093819, AC097537

Conserved Domains (1) summary

pfam01275
Location:2 → 184

Myelin_PLP; Myelin proteolipid protein (PLP or lipophilin)
NM_001388091.1 → NP_001375020.1 neuronal membrane glycoprotein M6-a isoform 5

Status: VALIDATED

Description

Transcript Variant: Variants 7 and 8 encode the same isoform (5).

Source sequence(s)

AC093819

Conserved Domains (1) summary

pfam01275
Location:2 → 184

Myelin_PLP; Myelin proteolipid protein (PLP or lipophilin)
NM_005277.5 → NP_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, Q92602

Related

ENSP00000280187.7, ENST00000280187.11

Conserved Domains (1) summary

pfam01275
Location:14 → 247

Myelin_PLP; Myelin proteolipid protein (PLP or lipophilin)
NM_201591.3 → NP_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)

AC093819, AC097537

Consensus CDS

CCDS3824.1

UniProtKB/Swiss-Prot

P51674, Q92602

Related

ENSP00000377268.2, ENST00000393658.7

Conserved Domains (1) summary

pfam01275
Location:14 → 247

Myelin_PLP; Myelin proteolipid protein (PLP or lipophilin)
NM_201592.3 → NP_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:3 → 236

Myelin_PLP; Myelin proteolipid protein (PLP or lipophilin)

RNA

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