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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
SLC5A6 ENST00000310574 24.67 27.18 23.97 1.38 1.24 1.09 1.14 1.14 1.05
EIF4B ENST00000262056 24.67 1.92 10.93 1.38 3.75 2.23 1.14 0.26 0.44
KBTBD4 ENST00000430070 24.68 51.81 36.36 1.38 0.61 0.85 1.13 1.87 1.87
USP3 ENST00000380324 24.68 3.47 11.70 1.38 3.39 2.21 1.13 0.29 0.47
GPR161 ENST00000537209 24.69 41.76 31.43 1.38 0.61 0.87 1.13 1.79 1.56
ZNF608 ENST00000306315 24.69 3.61 11.76 1.38 3.37 2.21 1.12 0.30 0.46
KIAA1598 ENST00000355371 24.70 23.08 22.00 1.38 1.46 1.18 1.12 0.91 0.97
SUV420H2 ENST00000255613 24.70 21.09 21.03 1.38 1.46 1.43 1.12 0.82 0.89
CUEDC2 ENST00000369937 24.71 32.95 26.99 1.38 0.82 1.00 1.12 1.47 1.28
SOD2 ENST00000538183 24.71 39.91 30.56 1.38 0.63 0.80 1.12 1.69 1.47
ATXN2L ENST00000395547 24.72 2.72 11.40 1.38 3.52 2.19 1.12 0.29 0.45
POGLUT1 ENST00000295588 24.72 48.53 34.81 1.38 0.65 0.90 1.12 2.02 1.76
TAX1BP1 ENST00000396319 24.73 31.99 26.46 1.38 0.92 1.00 1.12 1.48 1.25
NYAP2 ENST00000272907 24.74 35.69 28.37 1.38 0.78 0.80 1.12 1.57 1.29
RNF144A ENST00000320892 24.74 15.84 18.25 1.38 1.89 1.66 1.12 0.68 0.79
NAPB ENST00000377026 24.75 31.36 26.22 1.39 0.97 1.00 1.12 1.41 1.26
IPO11 ENST00000409296 24.75 19.59 20.25 1.39 1.43 1.48 1.12 0.74 0.88
LOX ENST00000231004 24.76 10.96 15.70 1.39 2.10 1.77 1.12 0.52 0.66
TMSB10 ENST00000233143 24.76 95.42 60.64 1.39 0.24 0.44 1.12 0.20 1.60
ARHGEF39 ENST00000378387 24.77 74.44 48.47 1.39 0.53 0.68 1.12 1.00 1.85
SPDYA ENST00000334056 24.77 25.17 23.08 1.39 1.32 1.20 1.12 1.03 1.00
PAXIP1 ENST00000404141 24.78 1.15 10.55 1.39 4.00 2.18 1.12 0.28 0.43
ENPP2 ENST00000259486 24.78 20.52 20.80 1.39 1.43 1.47 1.12 0.78 0.88
PLS1 ENST00000337777 24.79 34.42 27.77 1.39 0.81 0.90 1.12 1.56 1.27
GPSM2 ENST00000406462 24.79 47.29 34.33 1.39 0.66 0.87 1.12 2.00 1.77

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