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Aliases for GPC6 Gene

Aliases for GPC6 Gene

  • Glypican 6 2 3 5
  • Glypican Proteoglycan 6 2 3
  • Glypican-6 3
  • OMIMD1 3

External Ids for GPC6 Gene

Previous GeneCards Identifiers for GPC6 Gene

  • GC13P092238
  • GC13P088266
  • GC13P092715
  • GC13P091577
  • GC13P092677
  • GC13P093879
  • GC13P074476

Summaries for GPC6 Gene

Entrez Gene Summary for GPC6 Gene

  • The glypicans comprise a family of glycosylphosphatidylinositol-anchored heparan sulfate proteoglycans, and they have been implicated in the control of cell growth and cell division. The glypican encoded by this gene is a putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteases. Mutations in this gene are associated with omodysplasia 1. [provided by RefSeq, Nov 2016]

GeneCards Summary for GPC6 Gene

GPC6 (Glypican 6) is a Protein Coding gene. Diseases associated with GPC6 include Omodysplasia 1 and Omodysplasia. Among its related pathways are Metabolism of fat-soluble vitamins and Wnt Signaling Pathways: beta-Catenin-dependent Wnt Signaling. GO annotations related to this gene include heparan sulfate proteoglycan binding. An important paralog of this gene is GPC4.

UniProtKB/Swiss-Prot for GPC6 Gene

  • Cell surface proteoglycan that bears heparan sulfate. Putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteases (By similarity). Enhances migration and invasion of cancer cells through WNT5A signaling.

Gene Wiki entry for GPC6 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GPC6 Gene

Genomics for GPC6 Gene

Regulatory Elements for GPC6 Gene

Enhancers for GPC6 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH13F093861 1.1 Ensembl ENCODE 21.3 +635.3 635259 0.8 JUND BHLHE40 SIN3A FOS NFE2L2 GPC6 GPC6-AS2 GC13M094026
GH13F093867 0.5 ENCODE 21.3 +640.9 640887 1.1 FOS GPC6 GPC6-AS2 GC13M094026
GH13F093881 0.4 ENCODE 21 +655.3 655305 0.8 ZBTB48 ZNF366 BHLHE40 PRDM1 GPC6 GPC6-AS2 GC13M094026
GH13F093325 0.2 ENCODE 18.1 +99.8 99801 1.8 GATA3 JUND CUX1 GPC6 HNRNPA1P29 GC13M093240
GH13F093328 0.2 ENCODE 15.4 +102.3 102320 1.6 RAD21 GPC6 HNRNPA1P29 GC13M093240
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around GPC6 on UCSC Golden Path with GeneCards custom track

Promoters for GPC6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001511332 1175 4001 PKNOX1 SIN3A FEZF1 GLI4 ZNF48 ZNF2 YY1 ZNF121 GLIS2 ZNF263

Genomic Location for GPC6 Gene

Chromosome:
13
Start:
93,226,825 bp from pter
End:
94,408,020 bp from pter
Size:
1,181,196 bases
Orientation:
Plus strand

Genomic View for GPC6 Gene

Genes around GPC6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GPC6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GPC6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GPC6 Gene

Proteins for GPC6 Gene

  • Protein details for GPC6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y625-GPC6_HUMAN
    Recommended name:
    Glypican-6
    Protein Accession:
    Q9Y625
    Secondary Accessions:
    • A8K279
    • Q96SG5
    • Q96SG8
    • Q9H1P4

    Protein attributes for GPC6 Gene

    Size:
    555 amino acids
    Molecular mass:
    62736 Da
    Quaternary structure:
    No Data Available

neXtProt entry for GPC6 Gene

Post-translational modifications for GPC6 Gene

  • Glycosylation at Thr 374
  • Modification sites at PhosphoSitePlus

Other Protein References for GPC6 Gene

Antibody Products

No data available for DME Specific Peptides for GPC6 Gene

Domains & Families for GPC6 Gene

Gene Families for GPC6 Gene

Protein Domains for GPC6 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for GPC6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y625

UniProtKB/Swiss-Prot:

GPC6_HUMAN :
  • Belongs to the glypican family.
Family:
  • Belongs to the glypican family.
genes like me logo Genes that share domains with GPC6: view

Function for GPC6 Gene

Molecular function for GPC6 Gene

GENATLAS Biochemistry:
glypican 6,cell surface heparan sulfate proteoglycan,widely expressed with predominant expression in the adult ovary,liver and fetal kidney,juxtaposed to GPC5,involved in cellular growth control and differentiation
UniProtKB/Swiss-Prot Function:
Cell surface proteoglycan that bears heparan sulfate. Putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteases (By similarity). Enhances migration and invasion of cancer cells through WNT5A signaling.
UniProtKB/Swiss-Prot Induction:
Expression is induced by NFATC2.

Gene Ontology (GO) - Molecular Function for GPC6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043395 heparan sulfate proteoglycan binding IEA --
GO:1904929 coreceptor activity involved in Wnt signaling pathway, planar cell polarity pathway NAS 24431302
genes like me logo Genes that share ontologies with GPC6: view
genes like me logo Genes that share phenotypes with GPC6: view

Human Phenotype Ontology for GPC6 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for GPC6

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for GPC6 Gene

Localization for GPC6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GPC6 Gene

Cell membrane; Lipid-anchor, GPI-anchor; Extracellular side.
Secreted glypican-6: Secreted, extracellular space.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for GPC6 Gene COMPARTMENTS Subcellular localization image for GPC6 gene
Compartment Confidence
golgi apparatus 5
lysosome 5
nucleus 5
plasma membrane 5
vacuole 5
extracellular 4
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for GPC6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005615 extracellular space IEA --
GO:0005634 nucleus IDA 21630459
GO:0005796 Golgi lumen TAS --
genes like me logo Genes that share ontologies with GPC6: view

Pathways & Interactions for GPC6 Gene

SuperPathways for GPC6 Gene

genes like me logo Genes that share pathways with GPC6: view

Interacting Proteins for GPC6 Gene

Gene Ontology (GO) - Biological Process for GPC6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001523 retinoid metabolic process TAS --
GO:0006024 glycosaminoglycan biosynthetic process TAS --
GO:0006027 glycosaminoglycan catabolic process TAS --
GO:0016477 cell migration IDA 21871017
GO:0030203 glycosaminoglycan metabolic process TAS --
genes like me logo Genes that share ontologies with GPC6: view

No data available for SIGNOR curated interactions for GPC6 Gene

Transcripts for GPC6 Gene

Unigene Clusters for GPC6 Gene

Glypican 6:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for GPC6 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10
SP1: - -
SP2:
SP3:

Relevant External Links for GPC6 Gene

GeneLoc Exon Structure for
GPC6
ECgene alternative splicing isoforms for
GPC6

Expression for GPC6 Gene

mRNA expression in normal human tissues for GPC6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GPC6 Gene

This gene is overexpressed in Artery - Tibial (x5.1).

Protein differential expression in normal tissues from HIPED for GPC6 Gene

This gene is overexpressed in Ovary (12.1), Plasma (8.7), Cerebral cortex (8.6), Seminal vesicle (7.7), and Fetal testis (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for GPC6 Gene



NURSA nuclear receptor signaling pathways regulating expression of GPC6 Gene:

GPC6

SOURCE GeneReport for Unigene cluster for GPC6 Gene:

Hs.444329

mRNA Expression by UniProt/SwissProt for GPC6 Gene:

Q9Y625-GPC6_HUMAN
Tissue specificity: Widely expressed. High expression in fetal kidney and lung and lower expressions in fetal liver and brain. In adult tissues, very abundant in ovary, high levels also observed in liver, kidney, small intestine and colon. Not detected in peripheral blood leukocytes. Detected in breast cancer cells (at protein level).
genes like me logo Genes that share expression patterns with GPC6: view

Primer Products

No data available for Protein tissue co-expression partners for GPC6 Gene

Orthologs for GPC6 Gene

This gene was present in the common ancestor of animals.

Orthologs for GPC6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GPC6 34 35
  • 99.7 (n)
dog
(Canis familiaris)
Mammalia -- 35
  • 98 (a)
OneToMany
-- 35
  • 97 (a)
OneToMany
GPC6 34
  • 91.29 (n)
oppossum
(Monodelphis domestica)
Mammalia GPC6 35
  • 93 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GPC6 35
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Gpc6 34 16 35
  • 88.65 (n)
rat
(Rattus norvegicus)
Mammalia LOC691984 34
  • 87.87 (n)
cow
(Bos Taurus)
Mammalia GPC6 35
  • 61 (a)
OneToOne
chicken
(Gallus gallus)
Aves GPC6 34 35
  • 81.88 (n)
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 90 (a)
OneToMany
-- 35
  • 81 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia gpc6 34
  • 76.23 (n)
zebrafish
(Danio rerio)
Actinopterygii GPC6 (2 of 3) 35
  • 77 (a)
OneToMany
zgc:171629 34
  • 68.45 (n)
GPC6 (1 of 3) 35
  • 62 (a)
OneToMany
GPC6 (3 of 3) 35
  • 62 (a)
OneToMany
kny 34
fruit fly
(Drosophila melanogaster)
Insecta dlp 36 35
  • 43 (a)
worm
(Caenorhabditis elegans)
Secernentea gpn-1 35
  • 22 (a)
OneToMany
Species where no ortholog for GPC6 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)
  • 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)

Evolution for GPC6 Gene

ENSEMBL:
Gene Tree for GPC6 (if available)
TreeFam:
Gene Tree for GPC6 (if available)

Paralogs for GPC6 Gene

Paralogs for GPC6 Gene

(3) SIMAP similar genes for GPC6 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with GPC6: view

Variants for GPC6 Gene

Sequence variations from dbSNP and Humsavar for GPC6 Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type
rs121908440 Pathogenic 93,830,534(+) CAAAC(C/T)GAGTT intron-variant, reference, stop-gained
rs863223282 Pathogenic 94,027,795(+) GGGGG(-/C)TTCCC reference, frameshift-variant
rs794727797 Uncertain significance 94,306,132(+) AGTAT(A/T)CACAG intron-variant
rs1002468 -- 93,635,315(-) GGTAT(A/C)ATGTG intron-variant
rs10047752 -- 93,817,061(+) TCATA(G/T)AATCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for GPC6 Gene

Variant ID Type Subtype PubMed ID
dgv1014n106 CNV tandem duplication 24896259
dgv1015n106 CNV duplication 24896259
dgv571e212 CNV loss 25503493
dgv572e212 CNV loss 25503493
dgv573e212 CNV loss 25503493
dgv574e212 CNV loss 25503493
esv1057463 CNV insertion 17803354
esv1183301 CNV insertion 17803354
esv1437424 CNV deletion 17803354
esv2102591 CNV deletion 18987734
esv2435780 CNV deletion 19546169
esv2462615 CNV deletion 19546169
esv2530447 CNV deletion 19546169
esv2558321 CNV deletion 19546169
esv2661209 CNV deletion 23128226
esv2663873 CNV deletion 23128226
esv2667490 CNV deletion 23128226
esv2667781 CNV deletion 23128226
esv2677275 CNV deletion 23128226
esv2747828 CNV deletion 23290073
esv2747829 CNV deletion 23290073
esv2747831 CNV deletion 23290073
esv2747832 CNV deletion 23290073
esv2747833 CNV deletion 23290073
esv2747834 CNV deletion 23290073
esv2747835 CNV deletion 23290073
esv2747836 CNV deletion 23290073
esv2747837 CNV deletion 23290073
esv2747838 CNV deletion 23290073
esv2747839 CNV deletion 23290073
esv2747840 CNV deletion 23290073
esv2747842 CNV deletion 23290073
esv2751156 CNV loss 17911159
esv2759958 CNV loss 17122850
esv3143 CNV loss 18987735
esv3302619 CNV tandem duplication 20981092
esv3303710 CNV mobile element insertion 20981092
esv3307750 CNV mobile element insertion 20981092
esv3309712 CNV mobile element insertion 20981092
esv3327630 CNV insertion 20981092
esv3346862 CNV insertion 20981092
esv3360076 CNV duplication 20981092
esv3389916 CNV insertion 20981092
esv34004 CNV loss 18971310
esv3410705 CNV insertion 20981092
esv3425943 CNV insertion 20981092
esv3580825 CNV loss 25503493
esv3580826 CNV loss 25503493
esv3580828 CNV loss 25503493
esv3580829 CNV loss 25503493
esv3580830 CNV loss 25503493
esv3580833 CNV loss 25503493
esv3580834 CNV loss 25503493
esv3580835 CNV loss 25503493
esv3580836 CNV loss 25503493
esv3580837 CNV loss 25503493
esv3580839 CNV loss 25503493
esv3580850 CNV loss 25503493
esv3582694 CNV gain 25503493
esv3582716 CNV gain 25503493
esv3633196 CNV loss 21293372
esv3633197 CNV gain 21293372
esv3633198 CNV loss 21293372
esv3633199 CNV loss 21293372
esv3633200 CNV loss 21293372
esv3633201 CNV loss 21293372
esv3633202 CNV loss 21293372
esv3633204 CNV loss 21293372
esv3633207 CNV loss 21293372
esv3633212 CNV loss 21293372
esv3633213 CNV loss 21293372
esv3633214 CNV loss 21293372
esv3633217 CNV gain 21293372
esv3633218 CNV loss 21293372
esv3633223 CNV loss 21293372
esv3633225 CNV loss 21293372
esv3633227 CNV loss 21293372
esv3633229 CNV loss 21293372
esv3892424 CNV gain 25118596
esv3892428 CNV loss 25118596
esv3892429 CNV loss 25118596
esv9361 CNV gain 19470904
nsv1035144 CNV loss 25217958
nsv1048843 CNV loss 25217958
nsv1049455 CNV loss 25217958
nsv1050202 CNV loss 25217958
nsv1051276 CNV loss 25217958
nsv1052141 CNV gain 25217958
nsv1053695 CNV loss 25217958
nsv1070603 CNV deletion 25765185
nsv1116509 OTHER inversion 24896259
nsv1120288 CNV tandem duplication 24896259
nsv1127353 CNV deletion 24896259
nsv1129 CNV deletion 18451855
nsv1129549 CNV tandem duplication 24896259
nsv1130 CNV deletion 18451855
nsv1131 CNV insertion 18451855
nsv1135804 CNV deletion 24896259
nsv1138252 CNV deletion 24896259
nsv1147326 CNV deletion 26484159
nsv1153706 CNV insertion 26484159
nsv1154004 CNV deletion 26484159
nsv473254 CNV novel sequence insertion 20440878
nsv474799 CNV novel sequence insertion 20440878
nsv476626 CNV novel sequence insertion 20440878
nsv483085 CNV loss 15286789
nsv507724 OTHER sequence alteration 20534489
nsv507725 OTHER sequence alteration 20534489
nsv523214 CNV loss 19592680
nsv526048 CNV loss 19592680
nsv562749 CNV loss 21841781
nsv562750 CNV loss 21841781
nsv562751 CNV loss 21841781
nsv562752 CNV loss 21841781
nsv562753 CNV loss 21841781
nsv562754 CNV loss 21841781
nsv562755 CNV gain 21841781
nsv64659 CNV deletion 16902084
nsv64776 CNV deletion 16902084
nsv818989 CNV gain 17921354
nsv832683 CNV gain+loss 17160897
nsv832684 CNV loss 17160897
nsv957438 CNV deletion 24416366
nsv957483 CNV deletion 24416366
nsv977270 CNV duplication 23825009

Variation tolerance for GPC6 Gene

Residual Variation Intolerance Score: 28.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.34; 85.34% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for GPC6 Gene

Human Gene Mutation Database (HGMD)
GPC6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GPC6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GPC6 Gene

Disorders for GPC6 Gene

MalaCards: The human disease database

(5) MalaCards diseases for GPC6 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
omodysplasia 1
  • micromelic dysplasia congenita with dislocation of radius
omodysplasia
  • omodysplasia 2
atelosteogenesis
  • atelosteogenesis, type 1
simpson-golabi-behmel syndrome, type 1
  • simpson-golabi-behmel syndrome
body dysmorphic disorder
  • body dysmorphia
- elite association - COSMIC cancer census association via MalaCards
Search GPC6 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

GPC6_HUMAN
  • Omodysplasia 1 (OMOD1) [MIM:258315]: A rare autosomal recessive skeletal dysplasia characterized by facial dysmorphism and severe congenital micromelia with shortening and distal tapering of the humeri and femora, to give a club-like appearance. Typical facial features include a prominent forehead, frontal bossing, short nose with a depressed broad bridge, short columella, anteverted nostrils, long philtrum, and small chin. {ECO:0000269 PubMed:19481194}. Note=The disease is caused by mutations affecting the gene represented in this entry. Point mutations leading to protein truncation, as well as larger genomic rearrangements resulting in exon deletions, have been found in family segregating omodysplasia type 1. All mutations identified in individuals affected by omodysplasia could lead to the absence of a functional protein, the mutant RNAs being suspected to be nonsense-mediated mRNA decay (NMD) targets. Even if the mRNA escapes NMD and is translated, all mutations are expected to disrupt the three-dimensional protein structure and often to abolish multiple highly conserved cysteine residues.

Relevant External Links for GPC6

Genetic Association Database (GAD)
GPC6
Human Genome Epidemiology (HuGE) Navigator
GPC6
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
GPC6
genes like me logo Genes that share disorders with GPC6: view

No data available for Genatlas for GPC6 Gene

Publications for GPC6 Gene

  1. GPC6, a novel member of the glypican gene family, encodes a product structurally related to GPC4 and is colocalized with GPC5 on human chromosome 13. (PMID: 10329016) Paine-Saunders S. … Saunders S. (Genomics 1999) 2 3 4 22 64
  2. Mutations in the heparan-sulfate proteoglycan glypican 6 (GPC6) impair endochondral ossification and cause recessive omodysplasia. (PMID: 19481194) Campos-Xavier A.B. … Bonafe L. (Am. J. Hum. Genet. 2009) 3 4 22 64
  3. NFAT promotes carcinoma invasive migration through glypican-6. (PMID: 21871017) Yiu G.K. … Toker A. (Biochem. J. 2011) 3 4 64
  4. Heritability and genome-wide association analysis of renal sinus fat accumulation in the Framingham Heart Study. (PMID: 22044751) Foster M.C. … Fox C.S. (BMC Med. Genet. 2011) 3 46 64
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64

Products for GPC6 Gene

Sources for GPC6 Gene

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