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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
FKBP1C ENST00000370659 74.25 87.00 83.94 0.37 0.22 0.35 0.81 0.40 0.43
ADSSL1 ENST00000332972 74.26 44.48 59.71 0.37 0.63 0.49 0.82 1.98 1.66
OR2AP1 ENST00000321688 74.26 90.28 85.63 0.37 0.25 0.32 0.83 0.38 0.35
MMRN1 ENST00000394980 74.27 64.80 72.17 0.37 0.48 0.43 0.83 1.24 0.82
SDSL ENST00000403593 74.27 91.65 86.18 0.37 0.24 0.33 0.83 0.32 0.33
METTL2B ENST00000262432 74.28 65.95 72.86 0.37 0.54 0.40 0.83 1.23 0.81
PLEKHB1 ENST00000354190 74.28 55.80 66.76 0.37 0.52 0.53 0.83 1.58 1.20
TKTL2 ENST00000280605 74.29 64.08 71.74 0.37 0.49 0.46 0.83 1.20 0.81
SPRR1B ENST00000307098 74.29 95.16 87.84 0.37 0.23 0.24 0.83 0.21 0.32
OR2A12 ENST00000408949 74.30 77.99 79.41 0.37 0.42 0.39 0.83 0.77 0.52
PPL ENST00000345988 74.30 56.73 67.31 0.37 0.53 0.52 0.83 1.55 1.15
ZNF470 ENST00000330619 74.31 79.83 80.39 0.37 0.35 0.38 0.82 0.62 0.50
ZNF510 ENST00000375231 74.31 51.91 64.37 0.37 0.61 0.51 0.82 1.86 1.34
CHMP6 ENST00000325167 74.32 8.61 39.81 0.37 2.49 0.80 0.82 0.47 2.02
HNRNPA1L2 ENST00000342657 74.32 94.59 87.60 0.37 0.23 0.27 0.82 0.24 0.31
SNX22 ENST00000325881 74.33 65.77 72.75 0.37 0.54 0.43 0.82 1.22 0.81
COPE ENST00000262812 74.34 17.03 44.11 0.37 1.62 0.61 0.82 0.73 2.03
MFSD6L ENST00000329805 74.34 72.28 76.42 0.37 0.51 0.38 0.81 1.03 0.61
RNASET2 ENST00000508775 74.35 55.22 66.46 0.37 0.57 0.51 0.81 1.62 1.22
NOL7 ENST00000451315 74.35 71.11 75.73 0.37 0.49 0.38 0.81 1.07 0.64
TOR3A ENST00000367627 74.36 82.23 81.67 0.37 0.34 0.37 0.82 0.52 0.47
FASTKD3 ENST00000264669 74.36 64.81 72.26 0.37 0.48 0.44 0.82 1.24 0.82
NWD1 ENST00000524140 74.37 54.38 66.01 0.37 0.62 0.51 0.82 1.67 1.22
ATRAID ENST00000380171 74.37 63.33 71.34 0.37 0.48 0.43 0.82 1.31 0.87
RP11-385D13.1 ENST00000455584 74.38 63.81 71.65 0.37 0.49 0.44 0.82 1.22 0.83

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