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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
WIF1 ENST00000286574 47.01 60.00 52.82 0.56 0.53 0.61 1.81 1.37 1.88
DTWD1 ENST00000251250 47.01 83.37 66.93 0.56 0.27 0.53 1.81 0.47 1.19
RTCA ENST00000260563 47.02 60.05 52.84 0.56 0.53 0.61 1.81 1.37 1.88
ATG12 ENST00000509910 47.02 83.11 66.77 0.56 0.29 0.53 1.81 0.49 1.20
SH3BP2 ENST00000503393 47.03 60.04 52.85 0.56 0.53 0.61 1.81 1.37 1.88
RGS13 ENST00000391995 47.03 76.16 62.46 0.56 0.43 0.48 1.81 0.87 1.39
TAMM41 ENST00000273037 47.04 57.42 51.34 0.56 0.54 0.63 1.81 1.49 1.92
EFNA3 ENST00000368408 47.04 34.09 38.88 0.56 0.84 0.80 1.81 1.53 2.05
SYTL4 ENST00000455616 47.05 29.89 36.59 0.56 1.13 0.85 1.82 1.40 1.91
THNSL1 ENST00000524413 47.05 74.56 61.49 0.56 0.52 0.44 1.81 1.00 1.48
WDR19 ENST00000399820 47.06 29.08 36.20 0.56 1.14 0.87 1.81 1.32 1.84
BTN1A1 ENST00000244513 47.06 62.77 54.48 0.56 0.51 0.57 1.81 1.31 1.75
PNP ENST00000361505 47.07 62.11 54.09 0.57 0.54 0.59 1.81 1.36 1.76
ZNF304 ENST00000391705 47.07 31.75 37.65 0.57 0.95 0.82 1.81 1.47 2.00
IRG1 ENST00000377462 47.08 69.93 58.57 0.57 0.53 0.51 1.81 1.14 1.65
AIFM2 ENST00000307864 47.08 60.12 52.99 0.57 0.52 0.61 1.81 1.39 1.88
CKMT1A ENST00000413453 47.09 84.45 67.60 0.56 0.29 0.51 1.81 0.44 1.13
LIMS1 ENST00000542845 47.09 42.99 43.42 0.56 0.62 0.63 1.81 1.89 2.01
SEC31B ENST00000370345 47.10 57.31 51.32 0.56 0.54 0.63 1.82 1.49 1.91
RAVER2 ENST00000371072 47.11 43.62 43.73 0.56 0.62 0.61 1.82 1.96 2.02
TSC2 ENST00000219476 47.11 0.43 21.90 0.56 4.12 1.18 1.81 0.28 0.96
HSF4 ENST00000264009 47.12 61.56 53.77 0.56 0.54 0.62 1.81 1.41 1.80
ATP5E ENST00000243997 47.12 88.91 70.29 0.56 0.25 0.43 1.81 0.35 0.91
SPRYD7 ENST00000361840 47.13 67.97 57.47 0.56 0.52 0.51 1.81 1.18 1.65
ADM ENST00000528655 47.13 68.63 57.91 0.56 0.53 0.48 1.81 1.18 1.66

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