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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
UBQLN3 ENST00000311659 67.80 54.89 62.12 0.59 0.57 0.48 1.03 1.62 1.44
CNTF ENST00000361987 67.80 88.00 81.24 0.59 0.25 0.38 1.03 0.37 0.49
EFS ENST00000216733 67.81 67.43 69.85 0.59 0.54 0.46 1.03 1.20 0.92
NQO2 ENST00000338130 67.81 78.13 75.98 0.59 0.42 0.38 1.03 0.73 0.62
METTL8 ENST00000375258 67.82 71.93 72.53 0.59 0.51 0.46 1.03 1.07 0.83
C19orf40 ENST00000588258 67.82 89.61 82.09 0.59 0.27 0.35 1.03 0.37 0.46
OR2B3 ENST00000377173 67.83 74.29 73.84 0.59 0.53 0.42 1.03 1.01 0.71
TMEM252 ENST00000377311 67.83 82.29 78.32 0.59 0.34 0.38 1.03 0.53 0.54
TPRG1 ENST00000345063 67.84 88.97 81.76 0.59 0.25 0.35 1.03 0.35 0.47
PYGB ENST00000216962 67.84 48.87 58.41 0.59 0.63 0.52 1.03 2.03 1.65
PANX1 ENST00000227638 67.85 56.93 63.58 0.59 0.56 0.49 1.03 1.53 1.41
TMEM52B ENST00000298530 67.85 80.29 77.24 0.59 0.37 0.35 1.03 0.58 0.59
PLA2G4D ENST00000290472 67.86 51.54 60.12 0.59 0.63 0.47 1.03 1.87 1.61
IRAK1BP1 ENST00000369940 67.86 75.07 74.34 0.59 0.51 0.40 1.03 0.91 0.70
SIAE ENST00000263593 67.87 62.65 67.00 0.59 0.51 0.53 1.03 1.31 1.19
OR9Q1 ENST00000335397 67.87 83.93 79.22 0.59 0.28 0.38 1.03 0.47 0.54
ENOSF1 ENST00000340116 67.88 72.81 73.09 0.59 0.49 0.42 1.03 1.04 0.80
C1RL ENST00000266542 67.88 63.47 67.49 0.59 0.49 0.51 1.03 1.25 1.14
SH2D5 ENST00000444387 67.89 61.31 66.30 0.59 0.54 0.52 1.03 1.39 1.21
OR52B6 ENST00000345043 67.89 82.11 78.26 0.59 0.34 0.37 1.03 0.50 0.55
FAM120B ENST00000476287 67.90 39.52 53.14 0.59 0.68 0.61 1.03 1.63 1.88
CATSPER2 ENST00000321596 67.90 66.64 69.42 0.58 0.56 0.43 1.03 1.22 0.98
TEX14 ENST00000240361 67.91 51.22 60.00 0.58 0.65 0.48 1.03 1.91 1.63
UGT1A8 ENST00000305208 67.91 59.08 64.91 0.58 0.49 0.51 1.03 1.43 1.33
AIRE ENST00000291582 67.92 60.02 65.51 0.58 0.53 0.53 1.03 1.37 1.28

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