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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
LPAR3 ENST00000440886 37.97 29.96 32.17 0.92 1.09 0.91 1.73 1.42 1.60
RP5-1052I5.2 ENST00000370548 37.97 28.44 31.42 0.92 1.15 0.87 1.73 1.24 1.56
LHFPL5 ENST00000360215 37.98 76.05 56.87 0.92 0.43 0.51 1.73 0.86 1.70
RPAP3 ENST00000005386 37.98 31.43 32.89 0.92 0.96 0.86 1.72 1.42 1.67
PPY ENST00000591228 37.99 85.74 62.86 0.92 0.27 0.51 1.72 0.44 1.40
NUP85 ENST00000245544 37.99 2.87 18.36 0.92 3.51 1.66 1.73 0.28 0.80
SUPT3H ENST00000371460 38.00 66.80 51.54 0.92 0.54 0.62 1.73 1.23 1.93
TUBGCP5 ENST00000283645 38.00 35.03 34.74 0.92 0.76 0.90 1.73 1.58 1.75
IDH3B ENST00000380843 38.01 68.01 52.28 0.92 0.52 0.59 1.73 1.19 1.90
PHKB ENST00000323584 38.01 44.75 39.74 0.92 0.66 0.78 1.73 1.97 2.02
HELQ ENST00000295488 38.02 40.52 37.51 0.92 0.63 0.84 1.73 1.77 2.01
TMEM147 ENST00000222284 38.02 62.24 49.03 0.91 0.53 0.72 1.73 1.33 1.83
MAPK8IP2 ENST00000329492 38.03 1.13 17.45 0.91 4.01 1.62 1.73 0.28 0.76
KCTD12 ENST00000377474 38.04 44.47 39.61 0.91 0.63 0.78 1.73 1.98 2.04
DPY19L4 ENST00000414645 38.04 59.25 47.41 0.91 0.49 0.65 1.73 1.43 1.87
MPP3 ENST00000398389 38.05 33.63 34.02 0.91 0.85 0.89 1.73 1.55 1.72
ARHGEF15 ENST00000361926 38.05 35.55 35.00 0.91 0.77 0.89 1.73 1.58 1.73
SPATA2 ENST00000422556 38.06 12.44 23.35 0.91 2.06 1.20 1.73 0.59 0.99
SLC25A21 ENST00000331299 38.06 78.79 58.49 0.91 0.42 0.51 1.73 0.71 1.64
STAM2 ENST00000263904 38.07 38.56 36.40 0.91 0.72 0.84 1.73 1.66 1.87
PLEKHS1 ENST00000369310 38.07 85.88 63.05 0.91 0.28 0.51 1.73 0.43 1.39
RPRML ENST00000322329 38.08 79.55 58.91 0.91 0.38 0.49 1.73 0.66 1.65
OPTN ENST00000378748 38.08 67.88 52.21 0.91 0.52 0.61 1.73 1.17 1.89
WDR74 ENST00000525239 38.09 63.19 49.54 0.91 0.47 0.67 1.73 1.30 1.85
KIF13B ENST00000524189 38.09 23.14 28.74 0.91 1.46 0.80 1.73 0.90 1.33

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