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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
PDDC1 ENST00000319863 77.35 24.95 50.17 0.34 1.32 0.63 0.69 1.07 1.90
RASA4 ENST00000262940 77.36 66.25 74.70 0.34 0.53 0.40 0.69 1.20 0.67
SEC16A ENST00000313050 77.36 13.65 43.88 0.34 2.05 0.62 0.69 0.59 2.02
RAB17 ENST00000264601 77.37 54.53 67.86 0.34 0.59 0.51 0.69 1.65 1.12
TMEM212 ENST00000334567 77.37 89.90 86.79 0.34 0.25 0.29 0.68 0.37 0.31
SOX7 ENST00000304501 77.38 31.88 54.16 0.34 0.94 0.61 0.67 1.48 1.74
ERCC5 ENST00000355739 77.38 42.55 60.45 0.34 0.59 0.44 0.67 1.88 1.58
YIPF2 ENST00000586748 77.39 71.20 77.51 0.34 0.52 0.35 0.67 1.06 0.57
SULT1B1 ENST00000310613 77.39 71.12 77.47 0.34 0.49 0.35 0.67 1.07 0.57
PLD4 ENST00000392593 77.40 70.20 76.93 0.34 0.53 0.35 0.67 1.12 0.60
NDUFB2 ENST00000476279 77.40 92.72 88.24 0.34 0.29 0.23 0.67 0.30 0.30
C1orf186 ENST00000331555 77.41 82.07 83.12 0.34 0.34 0.30 0.67 0.51 0.40
DAGLB ENST00000297056 77.41 53.89 67.44 0.34 0.65 0.52 0.67 1.70 1.14
KRTDAP ENST00000338897 77.42 49.78 65.05 0.34 0.66 0.51 0.67 2.03 1.31
C15orf52 ENST00000559313 77.42 64.90 73.92 0.34 0.48 0.40 0.67 1.24 0.70
KNOP1 ENST00000219837 77.43 68.83 76.17 0.34 0.53 0.37 0.67 1.19 0.62
PRG4 ENST00000445192 77.43 38.39 57.95 0.34 0.75 0.48 0.67 1.71 1.66
SHISA5 ENST00000296444 77.44 77.61 80.84 0.34 0.42 0.39 0.67 0.79 0.51
KLK15 ENST00000598239 77.44 61.85 72.33 0.34 0.57 0.44 0.67 1.35 0.82
CLEC4G ENST00000328853 77.45 56.78 69.21 0.34 0.53 0.44 0.67 1.55 0.98
LCE1D ENST00000326233 77.45 94.46 89.07 0.34 0.23 0.19 0.67 0.24 0.26
C10orf62 ENST00000370640 77.46 95.49 89.57 0.34 0.24 0.18 0.67 0.21 0.23
SPRR2D ENST00000368757 77.47 95.28 89.50 0.34 0.23 0.18 0.67 0.21 0.23
FXYD4 ENST00000476166 77.47 78.63 81.41 0.34 0.40 0.37 0.67 0.74 0.48
CCDC137 ENST00000329214 77.48 71.50 77.69 0.34 0.53 0.38 0.67 1.06 0.55

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