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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
AP000695.1 ENST00000595927 87.83 99.74 96.60 0.23 0.17 0.08 0.36 0.11 0.08
HRCT1 ENST00000354323 86.83 99.74 94.93 0.24 0.17 0.09 0.40 0.11 0.11
ZNF860 ENST00000360311 86.91 99.73 95.70 0.24 0.17 0.07 0.39 0.11 0.11
FLJ14816 ENST00000593290 99.14 99.73 99.97 0.11 0.17 0.13 0.12 0.11 0.04
RNASE11 ENST00000610205 84.50 99.72 94.91 0.30 0.17 0.09 0.46 0.11 0.11
FPR1 ENST00000595042 84.44 99.72 94.86 0.30 0.17 0.09 0.46 0.11 0.11
IFNA2 ENST00000380206 94.77 99.71 98.97 0.10 0.17 0.10 0.11 0.11 0.04
C6orf195 ENST00000296847 98.56 99.71 99.92 0.10 0.17 0.12 0.11 0.11 0.04
HUS1B ENST00000380907 95.67 99.70 99.32 0.11 0.17 0.11 0.11 0.11 0.04
OR7G3 ENST00000305444 98.80 99.70 99.94 0.10 0.17 0.12 0.11 0.11 0.04
CXorf27 ENST00000341016 99.56 99.69 99.99 0.12 0.17 0.13 0.13 0.11 0.04
TCEB3C ENST00000330682 99.99 99.68 99.93 0.10 0.17 0.12 0.14 0.11 0.04
AC079210.1 ENST00000600820 75.17 99.68 90.08 0.38 0.17 0.18 0.76 0.12 0.22
AC024940.1 ENST00000313737 93.69 99.67 98.82 0.13 0.17 0.10 0.13 0.12 0.05
AL020996.1 ENST00000536896 93.66 99.67 98.81 0.13 0.17 0.10 0.13 0.12 0.05
AP003062.1 ENST00000597621 89.16 99.66 97.18 0.19 0.17 0.08 0.32 0.12 0.06
PYDC2 ENST00000518817 94.59 99.66 99.07 0.10 0.17 0.11 0.12 0.12 0.04
ZNF491 ENST00000323169 96.62 99.65 99.58 0.11 0.17 0.12 0.11 0.12 0.05
KRTAP19-5 ENST00000334151 85.64 99.65 95.43 0.28 0.17 0.08 0.46 0.12 0.11
USP29 ENST00000254181 94.94 99.64 98.76 0.10 0.17 0.10 0.12 0.12 0.05
AC013449.1 ENST00000599234 80.82 99.64 92.91 0.32 0.17 0.14 0.60 0.12 0.15
KRTAP4-3 ENST00000391356 89.57 99.63 96.64 0.16 0.16 0.08 0.30 0.12 0.08
FAM183B ENST00000409072 94.34 99.63 98.29 0.10 0.16 0.09 0.11 0.12 0.05
SPHAR ENST00000366688 93.53 99.62 98.76 0.13 0.16 0.10 0.14 0.12 0.05
C7orf13 ENST00000333319 93.52 99.62 98.48 0.13 0.16 0.10 0.14 0.12 0.05

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