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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
SLC17A1 ENST00000244527 94.87 72.69 86.98 0.10 0.47 0.28 0.11 1.04 0.30
KHDC1L ENST00000370388 94.87 75.68 88.40 0.10 0.44 0.22 0.11 0.90 0.30
H1FNT ENST00000335017 94.88 98.92 98.78 0.10 0.17 0.10 0.11 0.15 0.05
IGFN1 ENST00000335211 94.88 51.61 76.35 0.10 0.62 0.35 0.11 1.87 0.61
PSG2 ENST00000406487 94.89 97.45 98.43 0.10 0.22 0.10 0.12 0.19 0.05
NOBOX ENST00000467773 94.89 40.60 69.98 0.10 0.63 0.47 0.12 1.77 0.92
ZNF729 ENST00000601693 94.90 52.15 76.62 0.10 0.62 0.37 0.12 1.85 0.61
DSCR4 ENST00000328264 94.90 94.81 97.48 0.10 0.23 0.08 0.12 0.24 0.07
CD200R1 ENST00000308611 94.91 74.03 87.61 0.10 0.53 0.25 0.12 1.03 0.31
COX8C ENST00000342144 94.91 92.28 96.32 0.10 0.25 0.07 0.12 0.30 0.09
TRIM49B ENST00000332682 94.92 79.81 90.42 0.10 0.35 0.15 0.12 0.62 0.21
ZNF547 ENST00000282282 94.92 91.59 95.99 0.10 0.23 0.07 0.12 0.33 0.11
ZNF256 ENST00000282308 94.93 92.41 96.43 0.10 0.27 0.07 0.12 0.30 0.09
SRRM5 ENST00000607544 94.93 97.72 99.03 0.10 0.21 0.11 0.12 0.17 0.04
USP29 ENST00000254181 94.94 99.64 98.76 0.10 0.17 0.10 0.12 0.12 0.05
RTP4 ENST00000259030 94.94 56.37 78.94 0.10 0.52 0.39 0.12 1.53 0.52
CLLU1OS ENST00000378487 94.95 91.59 96.00 0.10 0.23 0.07 0.12 0.32 0.11
PRAMEF13 ENST00000376132 94.95 93.55 97.01 0.10 0.28 0.08 0.12 0.28 0.07
ZNF781 ENST00000358582 94.96 98.96 99.01 0.10 0.17 0.11 0.12 0.15 0.04
PSG11 ENST00000401740 94.96 92.68 96.61 0.10 0.29 0.08 0.12 0.30 0.08
POTEC ENST00000358970 94.97 69.03 85.34 0.10 0.54 0.34 0.12 1.14 0.36
SCAND1 ENST00000373991 94.97 78.30 89.74 0.10 0.43 0.18 0.12 0.74 0.23
OR2L2 ENST00000366479 94.98 98.17 98.72 0.10 0.20 0.10 0.12 0.16 0.05
C16orf71 ENST00000299320 94.98 80.26 90.68 0.10 0.37 0.15 0.12 0.58 0.20
HTN3 ENST00000530128 94.99 93.30 96.92 0.10 0.28 0.08 0.12 0.29 0.07

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