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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
ZNF45 ENST00000269973 61.21 43.44 51.46 0.62 0.61 0.63 1.32 1.95 1.91
OR6N1 ENST00000335094 61.22 88.10 77.88 0.62 0.24 0.38 1.32 0.38 0.54
EMG1 ENST00000261406 61.22 66.96 65.71 0.62 0.53 0.51 1.32 1.25 1.26
C1orf87 ENST00000371201 61.23 83.75 75.43 0.62 0.27 0.37 1.32 0.47 0.66
ENTPD3 ENST00000301825 61.23 83.58 75.32 0.62 0.27 0.37 1.32 0.47 0.65
SCO1 ENST00000255390 61.24 54.20 57.75 0.62 0.62 0.49 1.32 1.70 1.67
GJB7 ENST00000525899 61.24 94.13 81.05 0.62 0.25 0.39 1.32 0.25 0.49
TSACC ENST00000368255 61.25 80.16 73.48 0.62 0.37 0.40 1.32 0.59 0.76
MRPS33 ENST00000393008 61.25 83.08 75.09 0.63 0.29 0.39 1.32 0.49 0.67
C7orf26 ENST00000344417 61.26 12.03 34.82 0.63 2.06 0.90 1.31 0.57 1.76
PNPLA1 ENST00000394571 61.26 38.40 48.71 0.63 0.75 0.68 1.32 1.70 1.85
CPB1 ENST00000491148 61.27 84.13 75.69 0.63 0.27 0.38 1.32 0.45 0.64
SLC6A19 ENST00000304460 61.27 74.41 70.08 0.63 0.53 0.47 1.32 1.00 0.91
C3orf17 ENST00000314400 61.28 49.87 55.16 0.65 0.66 0.51 1.32 2.02 1.74
TRMT10B ENST00000297994 61.28 56.51 59.05 0.65 0.52 0.49 1.32 1.53 1.66
DHPS ENST00000210060 61.29 48.69 54.55 0.65 0.63 0.56 1.32 1.99 1.74
C1orf146 ENST00000370375 61.29 70.27 67.62 0.65 0.52 0.51 1.33 1.11 1.12
GOSR2 ENST00000225567 61.30 73.74 69.73 0.65 0.52 0.44 1.33 1.03 0.93
PPP1R14C ENST00000361131 61.30 74.01 69.88 0.65 0.54 0.46 1.33 1.03 0.92
RRH ENST00000317735 61.31 77.67 72.11 0.65 0.42 0.43 1.33 0.79 0.81
SLC35G1 ENST00000427197 61.31 35.12 46.97 0.65 0.76 0.70 1.34 1.58 1.87
FAM211A ENST00000470794 61.32 33.02 45.87 0.65 0.85 0.70 1.34 1.49 1.97
UBXN10 ENST00000375099 61.32 62.55 62.97 0.65 0.53 0.51 1.34 1.31 1.40
EFCAB11 ENST00000316738 61.33 68.64 66.71 0.66 0.53 0.54 1.34 1.18 1.20
MUS81 ENST00000308110 61.33 55.63 58.55 0.66 0.53 0.51 1.34 1.60 1.65

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