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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
AL136115.1 ENST00000391369 92.72 99.17 98.12 0.15 0.15 0.09 0.17 0.14 0.05
AC114546.1 ENST00000391457 92.73 99.17 98.45 0.15 0.15 0.10 0.17 0.14 0.05
AC090616.2 ENST00000398832 92.73 91.91 95.21 0.15 0.23 0.08 0.17 0.32 0.10
RP11-386G21.2 ENST00000522559 92.74 90.28 93.60 0.15 0.25 0.13 0.17 0.38 0.15
MRGPRG ENST00000332314 92.74 99.19 98.20 0.15 0.15 0.09 0.17 0.13 0.05
RP11-247C2.2 ENST00000514871 92.75 96.72 96.96 0.15 0.23 0.08 0.17 0.19 0.07
AC099552.4 ENST00000404289 92.75 77.83 88.48 0.15 0.42 0.22 0.17 0.79 0.29
C11orf44 ENST00000317019 92.76 88.49 93.07 0.15 0.23 0.14 0.17 0.36 0.15
KRTAP21-3 ENST00000444335 92.76 99.19 97.98 0.15 0.15 0.09 0.17 0.13 0.04
KIAA0087 ENST00000242109 92.77 95.44 97.02 0.15 0.24 0.08 0.17 0.20 0.07
MESDC1 ENST00000267984 92.77 17.94 54.88 0.15 1.53 0.51 0.17 0.73 1.75
TRIM49D1 ENST00000530311 92.78 93.62 96.10 0.15 0.28 0.07 0.17 0.28 0.11
SH3BGRL ENST00000373212 92.78 65.15 82.54 0.15 0.49 0.32 0.17 1.24 0.43
NANOGNB ENST00000382119 92.79 56.36 77.54 0.15 0.52 0.37 0.17 1.53 0.57
FAM106A ENST00000392176 92.79 99.21 98.47 0.15 0.15 0.10 0.17 0.13 0.05
AL161915.1 ENST00000391366 92.80 99.23 98.14 0.15 0.15 0.09 0.17 0.13 0.05
AGAP4 ENST00000448048 92.81 99.23 98.19 0.15 0.15 0.09 0.17 0.13 0.05
NPIPB5 ENST00000424340 92.81 99.24 97.42 0.15 0.15 0.08 0.17 0.13 0.07
SMIM18 ENST00000517349 92.82 84.29 91.56 0.15 0.28 0.15 0.17 0.44 0.18
SRSF10 ENST00000492112 92.82 87.42 92.86 0.15 0.23 0.14 0.17 0.40 0.15
AC007557.1 ENST00000456163 92.83 77.58 87.50 0.15 0.42 0.28 0.17 0.79 0.30
FAM195B ENST00000576730 92.83 71.08 85.46 0.15 0.49 0.33 0.17 1.07 0.35
CLEC19A ENST00000465414 92.84 83.30 91.41 0.15 0.27 0.15 0.17 0.48 0.18
C9orf53 ENST00000441769 92.84 99.26 97.96 0.15 0.15 0.09 0.16 0.13 0.04

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