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Connecting genetic risk to disease endpoints through the human blood plasma proteome

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Locus annotations

Locus 37

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
GPC5 cis Discovery rs342706 13:92,417,058 T/C 0.27 997 -0.861 0.040 1.2×10-83 -1.300 1.5×10-55 0.076
GPC5 cis Replication rs342706 13:92,417,058 A/G 0.29 337 -0.603 0.071 6.6×10-16 -1.170 1.2×10-7 0.018

 

Regional association plots

 

Boxplots and histograms for top associations

Glypican-5 (GPC5)

inverse-normalized probe levels log2 transformed probe levels raw probe levels
Discovery study
Replication study

Glypican-5 (GPC5)

Target (abbrv.) GPC5
Target (full name) Glypican-5
Somalogic ID (Sequence ID) SL012469 (4991-12_1)
Entrez Gene Symbol GPC5
UniProt ID P78333
UniProt Comment
  • Cell surface proteoglycan that bears heparan sulfate.
Reactome
  • A tetrasaccharide linker sequence is required for GAG synthesis
  • Defective B3GAT3 causes JDSSDHD
  • Defective B4GALT7 causes EDS, progeroid type
  • Defective EXT1 causes exostoses 1, TRPS2 and CHDS
  • Defective EXT2 causes exostoses 2
  • HS-GAG biosynthesis
  • HS-GAG degradation
  • Release of Hh-Np from the secreting cell
  • Retinoid metabolism and transport

All locus annotations are based on the sentinel SNP (rs342706) and 76 proxy variant(s) that is/are in linkage disequilibrium r2 ≥ 0.8. Linkage disequilibrium is based on data from the 1000 Genomes Project, phase 3 version 5, European population and was retrieved using SNiPA's Block Annotation feature.
Download the detailed results of SNiPA's block annotation (PDF)

Linked genes


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Genes hit or close-by
Potentially regulated genes
  • FABP5P4 fatty acid binding protein 5 pseudogene 4

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of NOTCH2NL in peripheral blood monocytes 1.6×10-7 20502693 (PMID) GRASP2 eQTL
Gene expression of DUSP6 in peripheral blood monocytes 1.3×10-6 20502693 (PMID) GRASP2 eQTL
Lung cancer in never smokers 5.9×10-6 20304703 (PMID) GRASP2 nonQTL
LUNG CANCER 6×10-6 20304703 (PMID) GWAS Catalog via SNiPA
Gene expression of CCDC137 in peripheral blood monocytes 6.5×10-6 20502693 (PMID) GRASP2 eQTL
Lung cancer (non-small cell lung cancer) in never smokers 3.6×10-5 20304703 (PMID) GRASP2 nonQTL
GPC5 expression levels 1.9×10-4 20304703 (PMID) GRASP2 nonQTL
Lung cancer (squamous cell carcinoma) 3×10-4 23341777 (PMID) GRASP2 nonQTL
Lung cancer (adenocarcinoma) in never smokers 4.8×10-4 20304703 (PMID) GRASP2 nonQTL

Extends role of GPC5 in lung cancer association to protein levels.

This locus harbours a replicated cis-pQTL with Glypican-5 (GPC5). Li et al. [PubMed] report rs2352028 at chromosome 13q31.3 in association with lung cancer in never smokers (combined odds ratio 1.46 [1.26-1.70], p=5.94×10-6). The authors also found a cis-eQTL of GPC5 in normal lung tissues, the high-risk allele being linked with lower expression. Moreover, the transcription level of GPC5 in normal lung tissue was twice that detected in matched lung adenocarcinoma tissue. rs2352028 is tagged by rs342706 (r2=0.95). Here SNP rs342706 is associated with GPC5 protein levels, with lower levels for the minor allele.

The information gathered here is a result of an attempt to keep track of all interesting information that we encountered while investigating these loci. Please bear in mind that the annotation given here is neither complete nor free of errors, and that all information provided here should be confirmed by additional literature research before being used as a basis for firm conclusions or further experiments.