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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
ZNF491 ENST00000323169 96.62 99.65 99.58 0.11 0.17 0.12 0.11 0.12 0.05
ERVV-1 ENST00000602168 92.29 98.88 97.85 0.15 0.17 0.09 0.19 0.14 0.04
KRTAP19-5 ENST00000334151 85.64 99.65 95.43 0.28 0.17 0.08 0.46 0.12 0.11
KRTAP13-1 ENST00000355459 96.13 98.88 99.29 0.11 0.17 0.11 0.11 0.14 0.04
USP29 ENST00000254181 94.94 99.64 98.76 0.10 0.17 0.10 0.12 0.12 0.05
RP11-156E8.1 ENST00000607453 92.28 98.87 98.22 0.15 0.17 0.09 0.19 0.14 0.05
AC013449.1 ENST00000599234 80.82 99.64 92.91 0.32 0.17 0.14 0.60 0.12 0.15
RP11-116D17.1 ENST00000547948 92.27 98.87 97.29 0.15 0.17 0.08 0.18 0.14 0.07
KRTAP4-3 ENST00000391356 89.57 99.63 96.64 0.16 0.16 0.08 0.30 0.12 0.08
OR13C5 ENST00000374779 96.76 98.86 99.45 0.11 0.16 0.11 0.11 0.14 0.05
FAM183B ENST00000409072 94.34 99.63 98.29 0.10 0.16 0.09 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
SPHAR ENST00000366688 93.53 99.62 98.76 0.13 0.16 0.10 0.14 0.12 0.05
ADAM29 ENST00000359240 97.15 98.85 99.55 0.10 0.16 0.12 0.11 0.14 0.05
MTRNR2L12 ENST00000600213 92.23 98.85 97.10 0.15 0.16 0.08 0.18 0.14 0.07
C7orf13 ENST00000333319 93.52 99.62 98.48 0.13 0.16 0.10 0.14 0.12 0.05
REXO1L1 ENST00000379010 92.21 98.84 98.09 0.15 0.16 0.09 0.18 0.14 0.05
DCAF4L2 ENST00000319675 86.66 99.61 95.90 0.24 0.16 0.07 0.41 0.12 0.10
AC079354.2 ENST00000594829 92.21 98.84 97.89 0.15 0.16 0.09 0.18 0.14 0.04
AC015989.2 ENST00000593319 93.51 99.61 97.88 0.13 0.16 0.09 0.14 0.12 0.04
USP17L2 ENST00000333796 95.80 98.83 99.18 0.11 0.16 0.11 0.11 0.14 0.04
RP11-89N17.1 ENST00000311067 93.50 99.60 97.16 0.13 0.16 0.08 0.14 0.12 0.07
TCEB3CL2 ENST00000591973 98.23 98.83 99.73 0.09 0.16 0.12 0.11 0.14 0.04
SBP1 ENST00000594414 96.41 99.60 99.20 0.10 0.16 0.11 0.11 0.12 0.04
KRTAP21-2 ENST00000333892 97.83 98.82 99.67 0.11 0.16 0.12 0.11 0.14 0.04

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