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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
C22orf24 ENST00000248984 99.55 88.55 96.88 0.12 0.24 0.08 0.13 0.36 0.07
CTD-2021H9.3 ENST00000549357 91.27 93.34 95.25 0.15 0.28 0.08 0.20 0.29 0.10
AL353354.2 ENST00000596102 90.12 97.78 96.88 0.16 0.21 0.08 0.25 0.17 0.07
ZNF117 ENST00000282869 97.33 87.73 95.26 0.10 0.24 0.08 0.11 0.37 0.10
KRTAP19-3 ENST00000334063 88.82 99.20 96.89 0.19 0.15 0.08 0.33 0.13 0.07
TSPY1 ENST00000451548 92.08 92.58 95.26 0.15 0.29 0.08 0.20 0.31 0.10
TAS2R10 ENST00000240619 88.56 99.55 96.89 0.20 0.16 0.08 0.34 0.13 0.07
PILRA ENST00000198536 98.66 86.43 95.27 0.10 0.24 0.08 0.11 0.42 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
BRICD5 ENST00000328540 88.37 96.77 95.28 0.20 0.23 0.08 0.35 0.19 0.10
AC104472.1 ENST00000399242 90.14 97.79 96.90 0.16 0.21 0.08 0.25 0.17 0.07
NPIPB6 ENST00000532254 89.54 95.59 95.28 0.16 0.23 0.08 0.30 0.21 0.10
C12orf42 ENST00000378113 96.31 91.90 96.91 0.12 0.23 0.08 0.11 0.32 0.07
IL13 ENST00000304506 99.95 85.21 95.29 0.10 0.25 0.08 0.14 0.45 0.10
ZNF530 ENST00000332854 98.18 90.08 96.91 0.11 0.25 0.08 0.11 0.37 0.07
FLJ20306 ENST00000601673 92.26 95.43 95.29 0.15 0.24 0.08 0.18 0.20 0.10
KLRF2 ENST00000535540 93.12 95.36 96.92 0.15 0.24 0.08 0.16 0.21 0.07
ASMT ENST00000381241 88.93 96.25 95.30 0.19 0.22 0.08 0.32 0.19 0.10
HTN3 ENST00000530128 94.99 93.30 96.92 0.10 0.28 0.08 0.12 0.29 0.07
NKG2-E ENST00000539033 98.31 86.87 95.30 0.09 0.22 0.08 0.10 0.41 0.10
PRR9 ENST00000368744 92.52 95.53 95.31 0.15 0.23 0.08 0.18 0.21 0.10
AC105020.1 ENST00000435356 90.75 98.10 96.93 0.16 0.20 0.08 0.23 0.16 0.07
ZNF844 ENST00000439326 95.27 89.91 95.32 0.10 0.25 0.08 0.11 0.37 0.10
AL109927.1 ENST00000601459 90.21 97.79 96.93 0.16 0.21 0.08 0.25 0.18 0.07

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