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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
PSAPL1 ENST00000319098 97.21 99.28 99.61 0.10 0.15 0.12 0.11 0.12 0.05
RPA4 ENST00000373040 97.52 98.86 99.61 0.10 0.16 0.12 0.11 0.14 0.05
C3orf27 ENST00000356020 98.98 97.56 99.60 0.11 0.22 0.12 0.12 0.19 0.05
OR7C1 ENST00000248073 98.45 97.99 99.60 0.10 0.20 0.12 0.11 0.17 0.05
TAS2R43 ENST00000531678 97.08 99.91 99.59 0.10 0.17 0.12 0.11 0.10 0.05
COLCA1 ENST00000532918 98.49 97.87 99.59 0.10 0.21 0.12 0.11 0.17 0.05
LINC00696 ENST00000541313 98.76 97.58 99.58 0.10 0.22 0.12 0.11 0.20 0.05
ZNF491 ENST00000323169 96.62 99.65 99.58 0.11 0.17 0.12 0.11 0.12 0.05
ZNF83 ENST00000597597 98.36 98.54 99.57 0.10 0.20 0.12 0.10 0.15 0.05
DEFB132 ENST00000382376 99.44 96.88 99.57 0.11 0.23 0.12 0.12 0.19 0.05
SPRR3 ENST00000331860 98.28 98.33 99.56 0.09 0.21 0.12 0.10 0.14 0.05
TEX19 ENST00000333437 98.34 97.84 99.56 0.09 0.21 0.12 0.10 0.17 0.05
PRR23C ENST00000413199 98.01 98.19 99.55 0.11 0.20 0.12 0.11 0.16 0.05
ADAM29 ENST00000359240 97.15 98.85 99.55 0.10 0.16 0.12 0.11 0.14 0.05
PNMA3 ENST00000447306 96.24 99.92 99.54 0.12 0.17 0.12 0.11 0.10 0.05
CEMP1 ENST00000382350 97.80 98.21 99.54 0.11 0.20 0.12 0.11 0.15 0.05
BLACE ENST00000378120 98.60 97.53 99.53 0.10 0.22 0.12 0.11 0.19 0.05
AL583828.1 ENST00000558378 97.88 99.57 99.52 0.11 0.16 0.12 0.11 0.12 0.05
MAGEC2 ENST00000247452 96.65 99.32 99.52 0.11 0.16 0.12 0.11 0.12 0.05
IRGM ENST00000522154 98.03 97.95 99.51 0.11 0.20 0.12 0.11 0.17 0.05
TAS2R30 ENST00000539585 98.06 97.88 99.51 0.11 0.21 0.12 0.11 0.17 0.05
PRKACG ENST00000377276 97.54 98.64 99.50 0.10 0.20 0.12 0.11 0.15 0.05
FSCB ENST00000340446 98.39 97.59 99.50 0.10 0.22 0.11 0.10 0.20 0.05
MRGPRX1 ENST00000302797 96.36 99.58 99.49 0.10 0.16 0.11 0.11 0.12 0.05
FAM218A ENST00000513876 96.46 99.42 99.49 0.10 0.16 0.11 0.11 0.12 0.05

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