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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
ARHGEF35 ENST00000378115 95.04 98.38 98.84 0.10 0.21 0.10 0.12 0.14 0.05
PRAMEF6 ENST00000376189 96.13 97.47 98.83 0.11 0.22 0.10 0.11 0.19 0.05
DEFB135 ENST00000382208 96.12 97.46 98.83 0.11 0.22 0.10 0.11 0.19 0.05
USP17L10 ENST00000417945 94.07 99.85 98.82 0.11 0.17 0.10 0.13 0.11 0.05
AC024940.1 ENST00000313737 93.69 99.67 98.82 0.13 0.17 0.10 0.13 0.12 0.05
C17orf82 ENST00000335108 94.28 99.11 98.81 0.10 0.15 0.10 0.12 0.14 0.05
AL020996.1 ENST00000536896 93.66 99.67 98.81 0.13 0.17 0.10 0.13 0.12 0.05
KRTAP9-1 ENST00000398470 95.33 98.05 98.80 0.10 0.20 0.10 0.11 0.16 0.05
MBD3L2 ENST00000381393 94.39 98.91 98.80 0.10 0.17 0.10 0.11 0.14 0.05
MAGEA6 ENST00000329342 94.86 98.38 98.79 0.10 0.21 0.10 0.11 0.14 0.05
AGAP8 ENST00000425119 90.91 98.18 98.79 0.16 0.20 0.10 0.20 0.16 0.05
H1FNT ENST00000335017 94.88 98.92 98.78 0.10 0.17 0.10 0.11 0.15 0.05
CT47B1 ENST00000371311 96.37 97.06 98.78 0.10 0.24 0.10 0.11 0.19 0.05
C17orf97 ENST00000360127 96.20 97.22 98.77 0.12 0.24 0.10 0.11 0.19 0.05
INSL4 ENST00000239316 97.86 95.54 98.77 0.11 0.23 0.10 0.11 0.21 0.05
USP29 ENST00000254181 94.94 99.64 98.76 0.10 0.17 0.10 0.12 0.12 0.05
SPHAR ENST00000366688 93.53 99.62 98.76 0.13 0.16 0.10 0.14 0.12 0.05
SCGB2A2 ENST00000227918 99.50 93.88 98.75 0.11 0.25 0.10 0.13 0.26 0.05
C6orf120 ENST00000332290 95.70 97.64 98.74 0.11 0.21 0.10 0.12 0.19 0.05
ZNF845 ENST00000458035 98.97 94.39 98.74 0.10 0.23 0.10 0.11 0.24 0.05
AC011484.1 ENST00000377652 95.66 98.47 98.73 0.11 0.21 0.10 0.11 0.14 0.05
SPANXN2 ENST00000370498 99.27 94.08 98.73 0.11 0.25 0.10 0.12 0.26 0.05
OR2L2 ENST00000366479 94.98 98.17 98.72 0.10 0.20 0.10 0.12 0.16 0.05
OR4A15 ENST00000314706 94.86 98.25 98.72 0.10 0.21 0.10 0.11 0.15 0.05
ICAM3 ENST00000160262 96.88 96.42 98.71 0.09 0.22 0.10 0.11 0.19 0.05

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