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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
C9orf163 ENST00000354376 95.46 99.35 98.68 0.11 0.16 0.10 0.11 0.12 0.05
ZNF80 ENST00000482457 88.74 99.35 96.27 0.19 0.16 0.07 0.33 0.12 0.09
FAM217B ENST00000358293 80.70 99.34 92.85 0.32 0.16 0.14 0.57 0.12 0.15
KRTAP19-6 ENST00000334046 96.04 99.34 99.37 0.11 0.16 0.11 0.11 0.12 0.04
ZFP42 ENST00000326866 96.32 99.33 99.43 0.12 0.16 0.11 0.11 0.12 0.05
TMEM78 ENST00000323223 92.97 99.33 98.55 0.16 0.16 0.10 0.16 0.12 0.05
MAGEC2 ENST00000247452 96.65 99.32 99.52 0.11 0.16 0.12 0.11 0.12 0.05
C22orf29 ENST00000405640 95.55 99.32 99.25 0.11 0.16 0.11 0.11 0.12 0.04
MRGPRE ENST00000436689 88.26 99.31 96.34 0.20 0.16 0.07 0.35 0.12 0.09
KRTAP12-4 ENST00000391618 98.04 99.31 99.79 0.11 0.16 0.12 0.11 0.12 0.04
KRTAP12-1 ENST00000391617 83.67 99.30 94.33 0.29 0.16 0.10 0.52 0.12 0.12
AL391152.1 ENST00000391612 92.92 99.30 98.53 0.16 0.16 0.10 0.16 0.12 0.05
TBC1D3G ENST00000341264 92.92 99.29 98.52 0.16 0.16 0.10 0.16 0.12 0.05
MTRNR2L2 ENST00000604882 92.89 99.29 98.22 0.15 0.15 0.09 0.16 0.12 0.05
DCAF8L1 ENST00000441525 84.26 99.28 94.56 0.30 0.15 0.09 0.47 0.12 0.11
PSAPL1 ENST00000319098 97.21 99.28 99.61 0.10 0.15 0.12 0.11 0.12 0.05
AP000867.1 ENST00000343767 92.85 99.27 98.50 0.15 0.15 0.10 0.16 0.13 0.05
OR5L1 ENST00000333973 97.94 99.27 99.77 0.11 0.15 0.12 0.11 0.13 0.04
C9orf53 ENST00000441769 92.84 99.26 97.96 0.15 0.15 0.09 0.16 0.13 0.04
TRIM60 ENST00000512596 97.06 99.26 99.33 0.10 0.15 0.11 0.11 0.13 0.04
EID2B ENST00000326282 95.58 99.25 98.94 0.11 0.15 0.10 0.11 0.13 0.04
IFNA6 ENST00000380210 82.83 99.25 93.87 0.30 0.15 0.09 0.55 0.13 0.12
CTB-186H2.3 ENST00000591669 84.60 99.24 94.51 0.29 0.15 0.10 0.46 0.13 0.12
NPIPB5 ENST00000424340 92.81 99.24 97.42 0.15 0.15 0.08 0.17 0.13 0.07
AGAP4 ENST00000448048 92.81 99.23 98.19 0.15 0.15 0.09 0.17 0.13 0.05

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