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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
ACKR2 ENST00000422265 61.73 78.24 72.67 0.71 0.43 0.43 1.29 0.74 0.81
HS3ST3B1 ENST00000360954 61.73 31.08 45.06 0.71 1.04 0.70 1.29 1.36 2.02
RWDD3 ENST00000370202 61.74 60.74 61.96 0.71 0.56 0.49 1.29 1.40 1.46
PROKR1 ENST00000303786 61.74 88.10 78.17 0.72 0.24 0.39 1.29 0.38 0.55
TWISTNB ENST00000222567 61.75 27.82 43.14 0.72 1.23 0.65 1.29 1.18 2.00
KRT16 ENST00000301653 61.75 84.87 76.41 0.72 0.27 0.38 1.29 0.43 0.62
ADAMTS18 ENST00000282849 61.76 50.85 56.01 0.72 0.63 0.49 1.29 1.92 1.77
CACNG1 ENST00000226021 61.76 89.80 79.10 0.72 0.27 0.39 1.29 0.37 0.53
FAM180A ENST00000338588 61.77 82.20 74.89 0.72 0.34 0.39 1.29 0.52 0.64
KRTAP3-1 ENST00000391588 61.77 93.39 80.91 0.72 0.28 0.39 1.29 0.28 0.51
CDC20B ENST00000381375 61.78 62.12 62.99 0.72 0.54 0.51 1.29 1.35 1.39
PCDHGA12 ENST00000252085 61.78 41.67 50.79 0.72 0.63 0.67 1.29 1.80 1.84
GCHFR ENST00000260447 61.79 86.25 77.18 0.72 0.27 0.35 1.30 0.43 0.59
OR10J3 ENST00000332217 61.79 92.41 80.45 0.72 0.27 0.39 1.30 0.30 0.50
AOX1 ENST00000374700 61.80 51.65 56.53 0.72 0.62 0.52 1.30 1.87 1.70
SYT5 ENST00000354308 61.80 48.00 54.47 0.72 0.62 0.57 1.29 2.00 1.75
SNRNP25 ENST00000383018 61.81 61.37 62.44 0.72 0.54 0.48 1.29 1.40 1.39
FAM227B ENST00000299338 61.81 78.48 72.90 0.72 0.42 0.40 1.29 0.74 0.81
TBL3 ENST00000568546 61.82 39.71 49.68 0.72 0.66 0.66 1.29 1.66 1.84
NOL10 ENST00000381685 61.83 20.98 39.75 0.71 1.44 0.78 1.29 0.83 2.03
OR10K2 ENST00000314902 61.83 95.94 82.25 0.71 0.22 0.35 1.29 0.20 0.45
TANGO2 ENST00000327374 61.84 50.90 56.10 0.71 0.63 0.49 1.29 1.94 1.77
SLC26A4 ENST00000265715 61.84 64.20 64.30 0.70 0.49 0.51 1.29 1.22 1.35
OPA3 ENST00000323060 61.85 76.89 71.97 0.70 0.43 0.42 1.29 0.80 0.80
MCEE ENST00000244217 61.85 76.23 71.57 0.70 0.43 0.44 1.29 0.85 0.83

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