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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
DEFA5 ENST00000330590 97.01 97.18 99.04 0.10 0.24 0.11 0.11 0.19 0.04
DEC1 ENST00000374016 99.67 94.53 99.05 0.12 0.23 0.11 0.13 0.24 0.04
C5orf55 ENST00000408966 95.69 98.31 99.05 0.11 0.21 0.11 0.12 0.14 0.04
USP17L17 ENST00000511568 94.24 99.98 99.06 0.10 0.18 0.11 0.13 0.09 0.04
PYDC2 ENST00000518817 94.59 99.66 99.07 0.10 0.17 0.11 0.12 0.12 0.04
TGIF2LY ENST00000321217 94.64 99.39 99.07 0.10 0.16 0.11 0.11 0.12 0.04
IL32 ENST00000525643 98.58 95.80 99.08 0.10 0.22 0.11 0.11 0.20 0.04
DEFB4A ENST00000302247 97.23 97.16 99.08 0.10 0.24 0.11 0.11 0.18 0.04
ZNF497 ENST00000311044 94.83 99.49 99.09 0.10 0.16 0.11 0.11 0.13 0.04
PF4V1 ENST00000226524 98.85 95.63 99.09 0.10 0.23 0.11 0.11 0.21 0.04
USP26 ENST00000511190 96.77 97.70 99.10 0.11 0.21 0.11 0.11 0.18 0.04
RARRES3 ENST00000255688 99.82 94.70 99.10 0.12 0.23 0.11 0.13 0.24 0.04
OR7E24 ENST00000456448 96.81 99.52 99.11 0.09 0.16 0.11 0.11 0.13 0.04
IFNA13 ENST00000449498 95.54 98.79 99.11 0.11 0.16 0.11 0.11 0.14 0.04
C21orf128 ENST00000329015 97.99 96.58 99.12 0.11 0.23 0.11 0.11 0.19 0.04
BIRC8 ENST00000426466 95.26 99.16 99.12 0.10 0.15 0.11 0.11 0.14 0.04
TAS2R42 ENST00000334266 96.92 98.48 99.13 0.09 0.21 0.11 0.11 0.14 0.04
AC026703.1 ENST00000326958 96.88 98.95 99.13 0.09 0.17 0.11 0.11 0.15 0.04
KRTAP19-1 ENST00000390689 96.12 99.94 99.14 0.11 0.17 0.11 0.11 0.10 0.04
IFNA1 ENST00000276927 95.79 98.62 99.14 0.11 0.20 0.11 0.11 0.15 0.04
MS4A6A ENST00000412309 98.37 96.30 99.15 0.10 0.22 0.11 0.10 0.19 0.04
TP53AIP1 ENST00000531399 98.15 96.55 99.15 0.11 0.22 0.11 0.11 0.19 0.04
NBPF10 ENST00000342960 97.40 97.32 99.16 0.10 0.23 0.11 0.11 0.19 0.04
FAM47C ENST00000358047 96.85 99.93 99.16 0.09 0.17 0.11 0.11 0.10 0.04
HRNR ENST00000368801 98.24 96.50 99.17 0.09 0.22 0.11 0.11 0.19 0.04

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