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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
UXT ENST00000335890 48.43 22.64 33.71 0.54 1.47 0.89 1.82 0.86 1.73
SEL1L2 ENST00000378072 48.43 65.28 56.67 0.54 0.51 0.52 1.82 1.24 1.71
WIZ ENST00000263381 48.44 8.74 26.74 0.54 2.48 0.99 1.82 0.48 1.27
GABRA6 ENST00000274545 48.44 71.91 60.77 0.53 0.51 0.44 1.82 1.07 1.61
PEX2 ENST00000419564 48.45 65.82 57.00 0.53 0.54 0.51 1.82 1.22 1.70
EPB41L5 ENST00000263713 48.45 19.97 32.42 0.53 1.46 0.91 1.82 0.73 1.61
AMPH ENST00000356264 48.46 28.34 36.50 0.53 1.16 0.85 1.82 1.22 1.90
FRRS1 ENST00000287474 48.46 44.15 44.96 0.53 0.61 0.68 1.82 1.96 2.04
PPA1 ENST00000373232 48.47 55.87 51.25 0.53 0.51 0.63 1.82 1.57 1.92
ASZ1 ENST00000284629 48.47 49.80 47.95 0.53 0.66 0.67 1.82 2.02 1.88
FA2H ENST00000219368 48.48 29.23 37.08 0.53 1.13 0.80 1.82 1.36 1.95
DCAF4L1 ENST00000333141 48.48 74.32 62.24 0.53 0.53 0.48 1.82 1.01 1.43
PROS1 ENST00000394236 48.49 28.96 36.94 0.52 1.15 0.80 1.82 1.31 1.94
GAK ENST00000314167 48.49 19.38 32.11 0.52 1.47 0.90 1.82 0.74 1.60
CD248 ENST00000311330 48.50 25.91 35.42 0.52 1.21 0.87 1.82 1.09 1.77
TMCO6 ENST00000394671 48.50 56.26 51.55 0.52 0.52 0.62 1.82 1.55 1.93
HYAL2 ENST00000447092 48.51 28.55 36.68 0.52 1.15 0.84 1.82 1.27 1.93
APIP ENST00000395787 48.52 87.60 70.36 0.52 0.23 0.43 1.82 0.37 0.91
BGN ENST00000331595 48.52 33.77 39.49 0.51 0.85 0.80 1.82 1.56 2.03
RXFP3 ENST00000330120 48.53 91.88 72.96 0.51 0.23 0.40 1.82 0.32 0.81
DNAH9 ENST00000262442 48.53 37.70 41.34 0.51 0.78 0.73 1.82 1.70 2.01
SAT2 ENST00000269298 48.54 80.84 66.39 0.51 0.35 0.52 1.82 0.57 1.20
CLCA1 ENST00000234701 48.54 37.48 41.23 0.51 0.78 0.75 1.81 1.67 2.01
LLGL2 ENST00000392550 48.55 35.91 40.49 0.51 0.80 0.80 1.81 1.58 2.04
RNASEH2B ENST00000336617 48.55 70.91 60.18 0.51 0.49 0.48 1.81 1.07 1.61

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