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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
BRICD5 ENST00000328540 88.37 96.77 95.28 0.20 0.23 0.08 0.35 0.19 0.10
RP11-127H5.1 ENST00000521923 89.94 94.99 95.27 0.18 0.23 0.08 0.27 0.21 0.10
AC003102.1 ENST00000399246 90.13 97.78 96.90 0.16 0.21 0.08 0.25 0.17 0.07
PILRA ENST00000198536 98.66 86.43 95.27 0.10 0.24 0.08 0.11 0.42 0.10
TAS2R10 ENST00000240619 88.56 99.55 96.89 0.20 0.16 0.08 0.34 0.13 0.07
TSPY1 ENST00000451548 92.08 92.58 95.26 0.15 0.29 0.08 0.20 0.31 0.10
KRTAP19-3 ENST00000334063 88.82 99.20 96.89 0.19 0.15 0.08 0.33 0.13 0.07
ZNF117 ENST00000282869 97.33 87.73 95.26 0.10 0.24 0.08 0.11 0.37 0.10
AL353354.2 ENST00000596102 90.12 97.78 96.88 0.16 0.21 0.08 0.25 0.17 0.07
CTD-2021H9.3 ENST00000549357 91.27 93.34 95.25 0.15 0.28 0.08 0.20 0.29 0.10
C22orf24 ENST00000248984 99.55 88.55 96.88 0.12 0.24 0.08 0.13 0.36 0.07
OR5D16 ENST00000378396 86.54 98.27 95.25 0.25 0.21 0.08 0.41 0.15 0.10
AP003733.1 ENST00000601917 90.07 97.76 96.87 0.16 0.21 0.08 0.26 0.17 0.07
C5orf60 ENST00000448248 99.95 85.06 95.24 0.10 0.25 0.08 0.14 0.45 0.10
KRTAP12-3 ENST00000397907 85.34 99.91 95.24 0.28 0.17 0.08 0.47 0.10 0.10
APOC4 ENST00000419266 95.12 92.98 96.86 0.10 0.28 0.08 0.12 0.30 0.07
TMEM221 ENST00000341130 93.42 92.10 95.23 0.13 0.24 0.08 0.15 0.32 0.10
CRYGN ENST00000337323 95.74 92.36 96.86 0.11 0.25 0.08 0.12 0.30 0.07
BLOC1S3 ENST00000433642 91.01 94.90 95.23 0.16 0.23 0.08 0.21 0.23 0.10
RP11-410N8.4 ENST00000375670 91.54 94.38 96.85 0.15 0.23 0.08 0.21 0.24 0.07
TMEM238 ENST00000444469 91.22 93.27 95.22 0.15 0.28 0.08 0.21 0.30 0.10
FKSG52 ENST00000412930 90.06 97.76 96.85 0.16 0.21 0.08 0.26 0.17 0.07
CGB8 ENST00000448456 89.40 95.56 95.22 0.16 0.23 0.08 0.32 0.21 0.10
RP11-315O6.2 ENST00000529278 90.04 97.75 96.84 0.16 0.21 0.08 0.26 0.17 0.07
AC090616.2 ENST00000398832 92.73 91.91 95.21 0.15 0.23 0.08 0.17 0.32 0.10

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