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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
CTD-3193O13.9 ENST00000539422 92.07 30.58 62.37 0.15 1.08 0.48 0.20 1.39 1.41
TSPY1 ENST00000451548 92.08 92.58 95.26 0.15 0.29 0.08 0.20 0.31 0.10
ARHGAP42 ENST00000298815 92.08 3.67 46.81 0.15 3.34 0.67 0.20 0.31 1.86
AC107021.1 ENST00000422482 92.09 98.79 98.14 0.15 0.16 0.09 0.20 0.14 0.05
CCL3L3 ENST00000378354 92.09 92.51 95.75 0.15 0.29 0.07 0.20 0.30 0.11
HMGN5 ENST00000358130 92.10 64.44 81.86 0.15 0.48 0.37 0.19 1.21 0.46
RP11-322E11.6 ENST00000589258 92.10 93.40 95.75 0.15 0.28 0.07 0.19 0.28 0.11
AGAP7 ENST00000374095 92.11 89.43 93.79 0.15 0.27 0.10 0.19 0.37 0.13
SULT1A3 ENST00000395137 92.11 89.72 93.90 0.15 0.27 0.09 0.19 0.37 0.11
AL079342.1 ENST00000369474 92.12 98.81 98.71 0.15 0.16 0.10 0.19 0.14 0.05
C11orf86 ENST00000308963 92.12 94.77 96.42 0.15 0.23 0.07 0.19 0.24 0.09
RP11-93B14.6 ENST00000370520 92.13 95.01 96.58 0.15 0.23 0.08 0.19 0.21 0.07
UBAP1L ENST00000559089 92.13 57.23 78.16 0.15 0.56 0.39 0.19 1.49 0.55
RP11-758M4.1 ENST00000523118 92.14 56.68 76.46 0.15 0.53 0.38 0.19 1.55 0.61
ZNF444 ENST00000337080 92.14 22.88 57.73 0.15 1.47 0.49 0.19 0.90 1.68
GSC2 ENST00000086933 92.15 94.63 96.35 0.15 0.23 0.07 0.19 0.24 0.09
AL592284.1 ENST00000538264 92.15 93.91 95.99 0.15 0.25 0.07 0.19 0.26 0.10
AC091801.1 ENST00000402115 92.16 87.03 92.56 0.15 0.22 0.14 0.19 0.40 0.15
CXorf30 ENST00000378657 92.16 26.01 59.63 0.15 1.20 0.49 0.19 1.10 1.68
PLGLB2 ENST00000359481 92.17 93.05 95.08 0.15 0.28 0.09 0.19 0.30 0.10
MUC22 ENST00000561890 92.17 37.21 66.59 0.15 0.77 0.52 0.19 1.66 1.20
SMIM17 ENST00000598409 92.18 83.83 91.18 0.15 0.27 0.15 0.19 0.47 0.18
B3GALT6 ENST00000379198 92.19 78.18 88.51 0.15 0.43 0.22 0.18 0.73 0.28
PINLYP ENST00000562365 92.19 50.30 73.96 0.15 0.66 0.40 0.18 1.96 0.69
FSBP ENST00000481490 92.20 63.18 81.28 0.15 0.47 0.38 0.18 1.30 0.48

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