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Genes Fold Enrichment Color Codes
  • Gene Name, Canonical Transcript - gene identifiers from gnomAD database (Build 37)
  • GeVIR % - gene rank measured in percentiles based on Gene Variation Intolerance Ranking (GeVIR) (low values indicate more variation intolerant genes, which is also true for "LOEUF %" and "VIRLoF %"). GeVIR is a method which we developed and applied on a list of 19,361 genes to sort them based on number, length and evolutionary conservation of regions without functional variants (i.e. between two missense, loss-of-function, insertion or delition variants) in gnomAD database (version 2.0.1). Only canonical transcripts were analysed.
  • LOEUF % - gene rank measured in percentiles based gnomAD loss-of-function observed/expected upper bound fraction (LOEUF) (see Figure 1). For more information about this metric, please read "Constraint" section of MacArthur Lab blog post. If you use this metric please cite gnomAD flagship paper and use most up-to-date values from gnomAD website.

    LoF observed/expected (o/e) upper Confidence Interval (CI)

    Figure 1. Screenshot of ELN gene constraint metrics from gnomAD browser

  • VIRLoF % - gene rank measured in percentiles based on both GeVIR and gnomAD LOEUF (shows the best overall performance, see Figure 2). If you use this metric please cite both GeVIR and gnomAD flagship paper.
  • GeVIR AD, LOEUF AD, VIRLoF AD, GeVIR AR, LOEUF AR, VIRLoF AR - to help users interpret gene ranks, we calculated fold enrichment of Autosomal Dominant (AD) and Autosomal Recessive (AR) genes with known molecular basis of disorder in OMIM in a range of +-5% of gene X (see Figure 2). Statistical significant fold enrichements (Fisher Exact Test p-value < 1e-5) are shown in bold in the table. For example CDK19 gene's GeVIR % is 2.37, so examined range is from 0 (2.37-5, rounded to minimal percentile) to 7.37% (2.37+5). Genes in this range are ~4 times more often (4.05 fold enrichement) associated with AD diseases and ~4 times less often (0.25 fold enrichement) associated with AR diseases. Both enrichment of AD genes and deficiency of AR genes is statistical significant. Thus GeVIR metric adds supportive evidence that CDK19 is more likely to be associated with AD than AR disease.

    Gene Percentiles AD AR Fold Enrichment

    Figure 2. Fold Enrichment of known Autosomal Dominant (AD) and Autosomal Recessive (AR) genes of each gene in the ranked lists (GeVIR, LOEUF, VIRLoF. AD genes are enriched among top ranked genes (lowest percentiles), whereas AR genes are enriched among middle ranked genes (approximetly 35-65 percentiles). Combined metric (VIRLoF, purple) shows the best perfornance, i.e. high ranked genes are more often associated with AD than AR diseases, low ranked genes are less often associated with both AD and AR diseases.
Gene Name Canonical Transcript GeVIR % LOEUF % VIRLoF % GeVIR AD LOEUF AD VIRLoF AD GeVIR AR LOEUF AR VIRLoF AR
C10orf40 ENST00000521074 92.72 99.16 97.13 0.15 0.15 0.08 0.17 0.14 0.07
AC010441.1 ENST00000600109 89.18 96.41 95.56 0.18 0.22 0.08 0.32 0.19 0.11
USP17L13 ENST00000429667 90.44 97.93 97.13 0.15 0.20 0.08 0.25 0.17 0.07
CXorf31 ENST00000377879 94.02 91.52 95.55 0.10 0.23 0.08 0.13 0.32 0.11
GOLGA6D ENST00000434739 88.85 96.70 95.55 0.19 0.23 0.08 0.32 0.19 0.11
AL139099.1 ENST00000539688 90.57 98.01 97.12 0.16 0.20 0.08 0.24 0.16 0.07
MBD3L5 ENST00000329753 92.56 92.64 95.54 0.15 0.29 0.08 0.18 0.31 0.11
LRG1 ENST00000306390 95.73 93.03 97.12 0.11 0.28 0.08 0.12 0.30 0.07
CTAGE1 ENST00000391403 87.58 97.85 95.54 0.23 0.21 0.08 0.37 0.17 0.11
NDUFV3 ENST00000354250 98.61 90.18 97.11 0.10 0.25 0.08 0.11 0.38 0.07
KRTAP9-3 ENST00000411528 87.87 97.62 95.53 0.23 0.22 0.08 0.36 0.20 0.11
CTD-2054N24.2 ENST00000560059 91.46 96.84 97.11 0.15 0.23 0.08 0.20 0.19 0.07
PUSL1 ENST00000379031 88.07 97.45 95.53 0.20 0.22 0.08 0.35 0.19 0.11
FAM111A ENST00000528737 88.70 96.81 95.52 0.19 0.23 0.08 0.34 0.19 0.11
C8orf56 ENST00000436771 90.40 97.92 97.10 0.15 0.20 0.08 0.25 0.17 0.07
KRTAP19-2 ENST00000334055 87.28 98.08 95.52 0.23 0.20 0.08 0.38 0.16 0.11
MTRNR2L12 ENST00000600213 92.23 98.85 97.10 0.15 0.16 0.08 0.18 0.14 0.07
ZNF582 ENST00000301310 98.73 86.78 95.51 0.10 0.24 0.08 0.11 0.40 0.11
AP000679.2 ENST00000319763 90.38 97.91 97.09 0.15 0.20 0.08 0.25 0.17 0.07
TBC1D3F ENST00000327454 89.69 95.72 95.51 0.16 0.23 0.08 0.28 0.20 0.11
GAGE10 ENST00000407599 95.73 92.94 97.09 0.11 0.29 0.08 0.12 0.30 0.07
PNMAL2 ENST00000599531 86.72 97.91 95.50 0.24 0.20 0.08 0.40 0.17 0.11
TEX22 ENST00000451127 93.15 95.26 97.08 0.15 0.23 0.08 0.16 0.21 0.07
TSPYL6 ENST00000317802 86.32 98.58 95.50 0.25 0.20 0.08 0.42 0.15 0.11
C6orf141 ENST00000529246 86.56 98.67 95.49 0.24 0.20 0.08 0.41 0.15 0.11

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