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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
RNASEK ENST00000548577 49.07 42.83 44.48 0.54 0.62 0.61 1.78 1.91 2.04
KIAA0825 ENST00000329378 49.08 80.80 66.63 0.54 0.35 0.52 1.78 0.57 1.20
SGSM1 ENST00000400359 49.08 24.13 34.79 0.54 1.35 0.90 1.78 0.98 1.77
SPAG1 ENST00000388798 49.09 38.32 41.93 0.54 0.75 0.68 1.78 1.71 2.01
FKBPL ENST00000375156 49.09 86.10 69.82 0.54 0.27 0.44 1.78 0.44 0.93
DDX20 ENST00000369702 49.10 56.48 52.02 0.54 0.52 0.62 1.78 1.54 1.94
OCIAD1 ENST00000381473 49.10 58.90 53.41 0.54 0.53 0.62 1.78 1.42 1.84
CCDC103 ENST00000417826 49.11 74.45 62.70 0.54 0.53 0.51 1.78 1.00 1.39
DAPK2 ENST00000261891 49.11 71.05 60.63 0.54 0.49 0.44 1.78 1.07 1.59
TEKT2 ENST00000207457 49.12 73.46 62.07 0.56 0.53 0.48 1.78 1.03 1.44
DNAJB1 ENST00000254322 49.12 52.84 49.97 0.56 0.65 0.61 1.78 1.80 1.90
SH3RF2 ENST00000511217 49.13 65.19 57.03 0.56 0.51 0.51 1.79 1.24 1.70
ATP6V0A4 ENST00000310018 49.13 52.09 49.52 0.57 0.61 0.67 1.79 1.85 1.84
EPM2A ENST00000367519 49.14 72.62 61.61 0.57 0.47 0.46 1.79 1.05 1.48
SLC38A11 ENST00000409149 49.15 83.48 68.30 0.57 0.27 0.51 1.79 0.46 1.07
THUMPD3 ENST00000345094 49.15 68.36 58.88 0.57 0.52 0.49 1.79 1.21 1.65
TBC1D31 ENST00000287380 49.16 46.44 46.45 0.57 0.73 0.67 1.80 2.03 1.92
IRS2 ENST00000375856 49.16 12.13 28.76 0.57 2.07 0.80 1.80 0.57 1.32
ZNF22 ENST00000298299 49.17 79.98 66.25 0.57 0.37 0.52 1.80 0.61 1.20
TMEM200C ENST00000581347 49.17 68.91 59.24 0.57 0.54 0.49 1.80 1.16 1.68
HIBADH ENST00000265395 49.18 45.91 46.23 0.57 0.76 0.67 1.80 2.02 1.94
PLEKHO2 ENST00000323544 49.18 30.27 37.99 0.57 1.09 0.85 1.80 1.39 2.03
FASTKD2 ENST00000236980 49.19 41.83 43.90 0.57 0.61 0.62 1.80 1.80 2.02
ATP6V0E1 ENST00000519374 49.19 51.81 49.37 0.57 0.61 0.70 1.80 1.87 1.84
DHRS7C ENST00000330255 49.20 77.87 64.98 0.57 0.42 0.51 1.79 0.79 1.32

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