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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
GBGT1 ENST00000372040 62.63 79.63 73.92 0.59 0.37 0.40 1.29 0.66 0.70
PTH2R ENST00000272847 62.64 75.58 71.66 0.59 0.44 0.44 1.29 0.90 0.83
SERPINB7 ENST00000398019 62.64 71.98 69.49 0.59 0.51 0.44 1.29 1.05 0.98
CA9 ENST00000378357 62.65 60.64 62.51 0.59 0.53 0.48 1.29 1.41 1.39
PIF1 ENST00000268043 62.65 72.63 69.88 0.59 0.47 0.46 1.29 1.05 0.92
RABL2B ENST00000395593 62.66 80.50 74.50 0.59 0.37 0.40 1.29 0.58 0.69
WDR96 ENST00000357060 62.66 36.15 48.29 0.59 0.82 0.67 1.29 1.60 1.87
NUP62 ENST00000596217 62.67 14.22 36.53 0.59 2.06 0.85 1.29 0.61 1.90
HYAL4 ENST00000223026 62.67 84.67 76.78 0.59 0.27 0.34 1.29 0.42 0.61
ANKRD6 ENST00000522441 62.68 45.63 53.57 0.59 0.73 0.63 1.29 2.01 1.80
C21orf59 ENST00000290155 62.68 57.85 60.87 0.59 0.57 0.43 1.29 1.47 1.59
TSEN54 ENST00000333213 62.69 46.72 54.23 0.59 0.73 0.59 1.29 1.96 1.75
TRAPPC2 ENST00000458511 62.69 89.30 79.31 0.59 0.27 0.39 1.29 0.37 0.53
SSPN ENST00000242729 62.70 65.68 65.79 0.59 0.53 0.51 1.29 1.22 1.26
MROH1 ENST00000528919 62.70 21.55 40.39 0.59 1.43 0.80 1.29 0.81 2.02
CDKN2B ENST00000276925 62.71 90.05 79.66 0.59 0.25 0.38 1.29 0.37 0.53
BTD ENST00000303498 62.71 65.37 65.63 0.59 0.52 0.51 1.29 1.25 1.29
WNT6 ENST00000233948 62.72 38.97 49.77 0.59 0.70 0.65 1.29 1.64 1.87
ETV7 ENST00000340181 62.72 79.02 73.67 0.59 0.40 0.40 1.28 0.70 0.72
HOXD11 ENST00000249504 62.73 81.17 74.85 0.59 0.34 0.39 1.28 0.55 0.64
COL13A1 ENST00000398978 62.73 40.73 50.78 0.59 0.63 0.66 1.28 1.78 1.84
CALHM1 ENST00000329905 62.74 80.29 74.41 0.59 0.37 0.40 1.28 0.58 0.70
NID2 ENST00000216286 62.74 27.08 43.28 0.59 1.23 0.65 1.28 1.12 2.01
CERK ENST00000216264 62.75 37.47 48.98 0.59 0.77 0.71 1.28 1.67 1.84
MYL7 ENST00000223364 62.76 79.68 74.04 0.59 0.37 0.38 1.28 0.65 0.69

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