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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
TTLL2 ENST00000239587 98.10 93.02 98.01 0.11 0.28 0.09 0.11 0.30 0.05
AL590822.2 ENST00000597060 91.81 98.62 98.01 0.14 0.20 0.09 0.20 0.15 0.05
C19orf48 ENST00000598463 96.58 98.96 99.41 0.11 0.17 0.11 0.11 0.15 0.05
CCDC144NL ENST00000327925 94.40 96.72 98.02 0.10 0.23 0.09 0.11 0.19 0.05
PRR23B ENST00000329447 96.91 98.57 99.42 0.09 0.20 0.11 0.11 0.15 0.05
AC139426.2 ENST00000435655 91.99 98.73 98.02 0.15 0.16 0.09 0.20 0.15 0.05
MRGPRX3 ENST00000396275 95.80 99.89 99.42 0.11 0.17 0.11 0.11 0.11 0.05
PRB1 ENST00000500254 96.48 94.66 98.03 0.10 0.23 0.09 0.11 0.24 0.05
AC124890.1 ENST00000399333 91.88 98.66 98.03 0.14 0.20 0.09 0.20 0.15 0.05
BLID ENST00000560104 96.18 99.49 99.43 0.11 0.16 0.11 0.11 0.13 0.05
C11orf89 ENST00000391480 92.49 99.02 98.04 0.15 0.15 0.09 0.18 0.15 0.05
ZFP42 ENST00000326866 96.32 99.33 99.43 0.12 0.16 0.11 0.11 0.12 0.05
C1orf61 ENST00000368243 99.91 91.26 98.04 0.10 0.23 0.09 0.14 0.34 0.05
DIRC1 ENST00000308100 96.69 99.86 99.44 0.11 0.17 0.11 0.11 0.11 0.05
TMPRSS11BNL ENST00000432593 93.89 97.23 98.05 0.11 0.24 0.09 0.13 0.19 0.05
IL3 ENST00000296870 99.82 95.99 99.44 0.12 0.22 0.11 0.13 0.20 0.05
PSG5 ENST00000366175 95.85 95.38 98.05 0.11 0.24 0.09 0.11 0.21 0.05
CST4 ENST00000217423 95.24 96.03 98.06 0.10 0.23 0.09 0.11 0.20 0.05
RP11-3B7.1 ENST00000440528 97.98 97.75 99.45 0.11 0.21 0.11 0.11 0.17 0.05
C2orf57 ENST00000313965 98.62 92.66 98.06 0.10 0.29 0.09 0.11 0.31 0.05
OR13C5 ENST00000374779 96.76 98.86 99.45 0.11 0.16 0.11 0.11 0.14 0.05
CXorf66 ENST00000370540 99.54 91.79 98.07 0.12 0.23 0.09 0.13 0.32 0.05
ZNF835 ENST00000537055 97.03 98.52 99.46 0.10 0.21 0.11 0.11 0.15 0.05
FOXD4L5 ENST00000377420 91.94 98.71 98.07 0.15 0.18 0.09 0.20 0.15 0.05
PRB2 ENST00000389362 98.52 97.34 99.46 0.10 0.23 0.11 0.11 0.19 0.05

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