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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
GFRA2 ENST00000524240 60.57 31.72 44.73 0.58 0.95 0.63 1.35 1.47 2.06
SMCO1 ENST00000397537 60.57 86.32 76.52 0.58 0.25 0.38 1.35 0.43 0.61
SETD4 ENST00000399215 60.58 67.78 65.78 0.58 0.52 0.51 1.35 1.18 1.26
ALKBH1 ENST00000216489 60.58 56.55 58.65 0.58 0.52 0.52 1.35 1.54 1.65
RMI2 ENST00000312499 60.59 95.25 81.28 0.58 0.23 0.38 1.35 0.21 0.48
ERAL1 ENST00000254928 60.59 56.61 58.70 0.58 0.53 0.51 1.35 1.55 1.65
C1orf226 ENST00000426197 60.60 14.79 35.80 0.58 1.95 0.85 1.34 0.62 1.78
ABCB8 ENST00000358849 60.60 61.05 61.48 0.58 0.54 0.44 1.34 1.39 1.48
MTMR7 ENST00000180173 60.61 53.10 56.67 0.58 0.66 0.52 1.34 1.77 1.71
SLC16A4 ENST00000369779 60.61 58.02 59.63 0.58 0.53 0.49 1.34 1.45 1.68
TMTC4 ENST00000342624 60.62 41.53 50.08 0.58 0.62 0.62 1.34 1.83 1.92
MARVELD2 ENST00000325631 60.62 64.96 64.07 0.58 0.49 0.52 1.34 1.24 1.37
FRMD8 ENST00000317568 60.63 26.53 41.81 0.58 1.19 0.72 1.34 1.12 2.01
ZNF526 ENST00000301215 60.63 24.42 40.67 0.58 1.30 0.81 1.34 1.00 2.04
GSG1 ENST00000432710 60.64 51.52 55.77 0.58 0.63 0.52 1.34 1.87 1.74
C1QTNF1 ENST00000339142 60.64 62.89 62.69 0.58 0.51 0.51 1.34 1.29 1.39
TNFSF10 ENST00000241261 60.65 33.94 46.00 0.57 0.84 0.68 1.34 1.56 1.96
LIPC ENST00000356113 60.65 53.41 56.88 0.57 0.65 0.51 1.33 1.70 1.70
TAGAP ENST00000367066 60.66 19.79 38.51 0.57 1.42 0.84 1.33 0.74 2.04
IQCH ENST00000335894 60.66 53.71 57.07 0.57 0.63 0.52 1.33 1.70 1.71
TMEM177 ENST00000424086 60.67 67.84 65.87 0.57 0.52 0.51 1.33 1.17 1.25
PJA1 ENST00000361478 60.67 16.95 37.04 0.57 1.66 0.80 1.33 0.73 1.95
PPP1R17 ENST00000342032 60.68 81.84 74.09 0.57 0.35 0.39 1.33 0.51 0.69
ACE ENST00000290866 60.68 59.20 60.46 0.57 0.49 0.44 1.33 1.44 1.58
BPIFC ENST00000397452 60.69 45.99 52.67 0.57 0.77 0.59 1.33 2.02 1.90

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