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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
SHB ENST00000377707 58.50 14.05 34.50 0.57 2.07 0.90 1.51 0.59 1.77
TEKT3 ENST00000395930 58.50 78.17 70.66 0.57 0.43 0.43 1.52 0.73 0.88
PPIC ENST00000306442 58.51 74.29 68.37 0.57 0.53 0.49 1.52 1.01 1.05
EIF2A ENST00000460851 58.51 45.40 51.04 0.57 0.68 0.66 1.52 2.00 1.88
TLL2 ENST00000357947 58.52 63.55 61.77 0.57 0.51 0.46 1.52 1.25 1.46
TRIM17 ENST00000366697 58.52 54.58 56.33 0.57 0.59 0.49 1.52 1.65 1.75
CMTM5 ENST00000359320 58.53 57.62 58.16 0.57 0.56 0.48 1.52 1.48 1.65
RETSAT ENST00000295802 58.54 62.05 60.91 0.57 0.56 0.43 1.52 1.37 1.58
ROM1 ENST00000278833 58.54 66.58 63.83 0.57 0.54 0.49 1.52 1.22 1.39
POLL ENST00000370162 58.55 59.70 59.40 0.57 0.52 0.49 1.52 1.39 1.71
OPN1LW ENST00000369951 58.55 12.33 33.60 0.57 2.07 0.87 1.52 0.59 1.72
DNASE2 ENST00000222219 58.56 50.32 53.90 0.57 0.66 0.61 1.52 1.96 1.77
PDRG1 ENST00000202017 58.56 81.34 72.63 0.57 0.33 0.46 1.52 0.54 0.81
ZFAND6 ENST00000261749 58.57 33.32 44.47 0.57 0.85 0.61 1.52 1.50 2.03
TMEM205 ENST00000354882 58.57 58.70 58.74 0.57 0.54 0.52 1.53 1.44 1.65
PPP6R1 ENST00000412770 58.58 12.50 33.72 0.57 2.07 0.89 1.53 0.59 1.73
CDKL2 ENST00000429927 58.58 75.16 68.92 0.57 0.49 0.46 1.53 0.91 1.04
POLR1C ENST00000372389 58.59 73.67 68.10 0.57 0.52 0.51 1.53 1.03 1.10
HEATR4 ENST00000553558 58.59 65.31 63.00 0.57 0.51 0.51 1.53 1.25 1.39
ALDH5A1 ENST00000348925 58.60 50.69 54.15 0.57 0.63 0.61 1.53 1.94 1.75
TOM1L1 ENST00000575882 58.60 54.68 56.45 0.57 0.58 0.52 1.53 1.64 1.70
MRPL10 ENST00000290208 58.61 53.46 55.73 0.57 0.65 0.53 1.52 1.72 1.74
GNGT2 ENST00000511277 58.61 80.56 72.26 0.57 0.37 0.44 1.51 0.57 0.82
SAPCD1 ENST00000415669 58.62 86.80 75.70 0.57 0.23 0.38 1.51 0.40 0.64
PROCR ENST00000216968 58.62 58.09 58.40 0.57 0.53 0.52 1.51 1.46 1.65

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