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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
TRPC1 ENST00000476941 10.08 23.94 14.78 2.04 1.38 1.95 0.53 0.95 0.62
BCL10 ENST00000370580 10.08 37.93 22.13 2.02 0.78 1.16 0.54 1.70 0.97
MFSD2A ENST00000372809 10.09 25.79 15.77 2.02 1.23 1.77 0.54 1.05 0.66
BLOC1S2 ENST00000370372 10.09 67.80 37.24 2.02 0.52 0.82 0.54 1.18 1.99
MSL1 ENST00000579565 10.10 2.99 3.88 2.02 3.47 3.75 0.54 0.28 0.23
FNTB ENST00000246166 10.10 22.17 13.78 2.02 1.52 2.07 0.54 0.81 0.57
ENC1 ENST00000302351 10.11 23.22 14.38 2.02 1.43 2.01 0.54 0.92 0.59
ZNF287 ENST00000395824 10.11 18.50 11.92 2.02 1.49 2.28 0.54 0.76 0.46
ARHGEF12 ENST00000397843 10.12 4.66 4.73 2.02 3.26 3.68 0.54 0.31 0.25
RP11-211G3.3 ENST00000449623 10.12 83.84 45.67 2.02 0.28 0.68 0.54 0.47 1.99
VWC2L ENST00000312504 10.13 45.35 25.88 2.02 0.68 1.01 0.54 1.99 1.23
AZIN1 ENST00000337198 10.13 8.63 6.74 2.02 2.49 3.00 0.54 0.47 0.32
PANK3 ENST00000239231 10.14 48.73 27.56 2.02 0.63 0.96 0.53 1.99 1.27
SF3B2 ENST00000322535 10.14 7.03 5.84 2.02 2.57 3.30 0.53 0.37 0.28
NUPL1 ENST00000381736 10.15 15.18 10.23 2.02 1.90 2.21 0.53 0.67 0.42
ELF3 ENST00000359651 10.15 13.64 9.34 2.02 2.05 2.32 0.53 0.59 0.38
PPP2R2B ENST00000336640 10.16 12.32 8.57 2.02 2.07 2.52 0.53 0.59 0.36
ATP6V1F ENST00000492758 10.16 83.63 45.61 2.01 0.27 0.68 0.54 0.47 1.98
EHBP1 ENST00000263991 10.17 14.90 10.11 2.01 1.94 2.24 0.54 0.62 0.42
CSNK1G1 ENST00000303052 10.18 6.83 5.77 2.02 2.62 3.31 0.54 0.37 0.28
SLC41A1 ENST00000367137 10.18 20.83 13.10 2.02 1.43 2.10 0.54 0.83 0.52
FAM46A ENST00000320172 10.19 16.91 11.20 2.02 1.64 2.15 0.54 0.71 0.45
PLP1 ENST00000418604 10.19 16.19 10.79 2.02 1.81 2.19 0.54 0.70 0.43
SNX27 ENST00000368843 10.20 5.16 4.95 2.02 3.20 3.69 0.54 0.32 0.25
GLTSCR1L ENST00000314073 10.20 0.39 2.75 2.02 4.14 4.03 0.54 0.28 0.23

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