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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
ZNF763 ENST00000343949 97.48 79.79 91.51 0.10 0.35 0.15 0.11 0.62 0.18
MRGPRX2 ENST00000329773 98.74 99.21 99.89 0.10 0.15 0.12 0.11 0.13 0.04
GSTT2B ENST00000290765 97.49 39.24 70.68 0.10 0.70 0.43 0.11 1.64 0.88
NBPF1 ENST00000430580 99.99 57.03 81.87 0.10 0.56 0.37 0.14 1.52 0.46
C3orf56 ENST00000398112 98.74 98.08 99.68 0.10 0.20 0.12 0.11 0.16 0.04
LRRC37A2 ENST00000576629 97.49 46.30 74.81 0.10 0.73 0.39 0.11 2.05 0.66
ZNF595 ENST00000526473 100.00 67.01 86.68 0.10 0.53 0.30 0.14 1.24 0.33
CD300LB ENST00000392621 98.75 83.27 93.80 0.10 0.28 0.10 0.11 0.47 0.13
ZDHHC11 ENST00000283441 97.50 80.85 91.94 0.10 0.35 0.14 0.11 0.57 0.16
AC012493.2 ENST00000595083 93.98 99.80 98.64 0.10 0.17 0.10 0.13 0.11 0.05
GJD3 ENST00000578689 93.98 94.40 95.95 0.10 0.23 0.07 0.13 0.24 0.10
C2orf81 ENST00000290390 93.99 43.58 71.23 0.10 0.62 0.44 0.13 1.96 0.86
AC112715.2 ENST00000445534 93.99 83.92 91.78 0.10 0.28 0.14 0.13 0.47 0.18
TIGD1 ENST00000408957 94.00 66.50 83.66 0.10 0.57 0.34 0.13 1.22 0.40
MAGED4 ENST00000375626 94.00 92.20 93.84 0.10 0.25 0.10 0.13 0.31 0.12
C14orf164 ENST00000399910 94.01 62.07 79.44 0.10 0.56 0.39 0.13 1.36 0.52
MTRNR2L10 ENST00000545075 94.01 99.82 98.95 0.10 0.17 0.10 0.13 0.11 0.04
DEFB107B ENST00000355602 94.02 99.84 97.73 0.10 0.17 0.09 0.13 0.11 0.05
CXorf31 ENST00000377879 94.02 91.52 95.55 0.10 0.23 0.08 0.13 0.32 0.11
CITED4 ENST00000372638 94.03 90.21 94.88 0.10 0.25 0.09 0.13 0.38 0.11
FAM163B ENST00000496132 94.03 93.64 96.19 0.10 0.28 0.07 0.13 0.28 0.10
DDX3Y ENST00000336079 94.04 11.11 49.45 0.10 2.09 0.70 0.13 0.53 1.83
C19orf35 ENST00000342063 94.04 89.35 94.45 0.10 0.27 0.10 0.13 0.37 0.12
THEM6 ENST00000336138 94.05 87.22 93.36 0.10 0.20 0.11 0.13 0.41 0.15
DAZ2 ENST00000382440 94.06 93.78 96.68 0.10 0.27 0.08 0.13 0.26 0.08

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