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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
PIK3R6 ENST00000311434 75.16 76.06 78.83 0.38 0.43 0.39 0.76 0.86 0.52
HRH4 ENST00000256906 75.16 76.96 79.33 0.38 0.43 0.39 0.76 0.79 0.53
SRRD ENST00000215917 75.17 78.94 80.36 0.38 0.40 0.38 0.76 0.69 0.50
AC079210.1 ENST00000600820 75.17 99.68 90.08 0.38 0.17 0.18 0.76 0.12 0.22
TMEM31 ENST00000319560 75.18 94.10 87.77 0.38 0.25 0.24 0.76 0.26 0.32
DLEC1 ENST00000308059 75.18 48.71 62.98 0.38 0.63 0.51 0.76 1.99 1.40
DNAH11 ENST00000328843 75.19 34.99 54.69 0.38 0.75 0.56 0.76 1.56 1.73
UTP14C ENST00000521776 75.19 31.89 52.89 0.38 0.94 0.61 0.76 1.48 1.87
HES3 ENST00000377898 75.20 67.52 74.22 0.38 0.54 0.39 0.76 1.20 0.69
ABHD15 ENST00000307201 75.20 78.51 80.19 0.38 0.42 0.35 0.76 0.74 0.52
RASAL3 ENST00000343625 75.21 42.97 59.35 0.38 0.62 0.51 0.76 1.90 1.69
STS ENST00000217961 75.21 22.86 47.87 0.38 1.46 0.66 0.76 0.89 1.90
OR2M4 ENST00000306687 75.22 84.96 83.44 0.38 0.25 0.33 0.76 0.45 0.40
PCDHB6 ENST00000231136 75.22 74.46 78.03 0.38 0.53 0.38 0.76 0.99 0.54
PPP1R14B ENST00000309318 75.23 81.40 81.70 0.38 0.33 0.35 0.76 0.54 0.47
CLEC4E ENST00000299663 75.23 71.45 76.45 0.38 0.53 0.38 0.76 1.05 0.61
CASP1 ENST00000533400 75.24 46.45 61.56 0.38 0.73 0.46 0.76 2.02 1.48
ZNF227 ENST00000313040 75.24 50.36 64.07 0.38 0.66 0.52 0.76 1.96 1.37
CD40 ENST00000372285 75.25 19.65 46.16 0.38 1.43 0.67 0.76 0.74 1.97
ADH1B ENST00000305046 75.25 68.03 74.57 0.38 0.52 0.40 0.76 1.18 0.69
ITM2A ENST00000373298 75.26 53.42 65.96 0.37 0.65 0.51 0.76 1.70 1.24
NDUFAF3 ENST00000326925 75.26 56.91 68.05 0.37 0.56 0.51 0.76 1.53 1.10
RARRES1 ENST00000237696 75.27 83.28 82.69 0.37 0.27 0.32 0.76 0.47 0.42
IGSF10 ENST00000282466 75.28 67.83 74.47 0.37 0.52 0.40 0.76 1.17 0.69
C4BPB ENST00000243611 75.28 70.79 76.04 0.37 0.49 0.38 0.76 1.08 0.62

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