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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
MTNR1B ENST00000257068 72.19 69.13 73.46 0.34 0.56 0.40 0.81 1.12 0.76
RHOF ENST00000267205 72.19 70.13 73.95 0.34 0.53 0.40 0.81 1.11 0.69
ITGAE ENST00000263087 72.20 49.05 61.29 0.34 0.67 0.44 0.81 2.03 1.48
ATP6V1G3 ENST00000281087 72.20 67.15 72.38 0.34 0.54 0.44 0.81 1.22 0.83
IQUB ENST00000466202 72.21 55.12 65.10 0.34 0.58 0.51 0.80 1.63 1.31
OR51G1 ENST00000321961 72.21 78.81 78.76 0.34 0.42 0.39 0.80 0.71 0.53
PDILT ENST00000302451 72.22 42.89 57.49 0.34 0.62 0.52 0.80 1.91 1.65
GNG5P2 ENST00000372054 72.22 91.18 85.07 0.34 0.24 0.33 0.80 0.35 0.38
CCDC124 ENST00000597436 72.23 42.50 57.25 0.34 0.59 0.52 0.80 1.87 1.70
OR10G8 ENST00000431524 72.23 80.14 79.45 0.34 0.37 0.39 0.80 0.59 0.52
RP5-850E9.3 ENST00000488788 72.24 82.95 80.96 0.34 0.30 0.39 0.80 0.49 0.50
IDUA ENST00000247933 72.24 57.44 66.50 0.34 0.56 0.51 0.80 1.48 1.21
PMS2 ENST00000265849 72.25 72.03 75.06 0.34 0.52 0.39 0.80 1.03 0.66
XRRA1 ENST00000340360 72.25 43.84 58.11 0.34 0.61 0.48 0.79 1.97 1.65
TSEN2 ENST00000284995 72.26 62.24 69.39 0.34 0.53 0.43 0.79 1.33 0.99
PPP1R36 ENST00000298705 72.26 65.49 71.37 0.34 0.54 0.43 0.79 1.23 0.86
C5orf58 ENST00000521850 72.27 87.91 83.44 0.34 0.25 0.33 0.79 0.37 0.40
ZNF667 ENST00000504904 72.27 44.88 58.66 0.34 0.68 0.52 0.79 1.99 1.65
KIF7 ENST00000394412 72.28 47.99 60.69 0.34 0.62 0.44 0.79 2.00 1.61
CNN2 ENST00000263097 72.28 39.58 55.61 0.34 0.68 0.53 0.80 1.65 1.73
JMJD7 ENST00000397299 72.29 52.81 63.81 0.34 0.65 0.49 0.80 1.80 1.38
ERVW-1 ENST00000493463 72.29 98.43 88.58 0.34 0.21 0.22 0.80 0.14 0.28
FAM183A ENST00000335282 72.30 66.88 72.28 0.34 0.53 0.43 0.80 1.24 0.82
PLA2G2F ENST00000375102 72.31 91.03 85.04 0.34 0.25 0.33 0.80 0.36 0.39
DRD5 ENST00000304374 72.31 95.98 87.35 0.34 0.22 0.28 0.80 0.20 0.31

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