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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
C4A ENST00000428956 52.04 71.77 62.90 0.59 0.51 0.51 1.83 1.07 1.40
DUSP12 ENST00000367943 52.05 47.35 48.60 0.59 0.66 0.67 1.84 2.00 1.85
TLX2 ENST00000233638 52.05 44.59 47.05 0.59 0.65 0.68 1.84 1.97 1.88
ADRA1A ENST00000380586 52.06 77.05 66.23 0.59 0.42 0.52 1.84 0.78 1.20
PRRT2 ENST00000567659 52.06 29.31 39.02 0.59 1.14 0.78 1.84 1.36 2.06
SSBP4 ENST00000270061 52.07 21.82 35.10 0.59 1.47 0.86 1.83 0.81 1.75
LY6G6F ENST00000375832 52.07 70.47 62.03 0.59 0.52 0.48 1.83 1.08 1.44
ZBTB47 ENST00000232974 52.08 1.90 25.06 0.59 3.74 1.05 1.82 0.26 1.15
C1orf198 ENST00000366663 52.08 55.99 53.45 0.59 0.49 0.62 1.82 1.56 1.83
PDE8A ENST00000310298 52.09 27.05 37.79 0.59 1.23 0.84 1.82 1.12 2.01
MERTK ENST00000295408 52.09 39.66 44.34 0.59 0.68 0.61 1.82 1.65 2.04
ZFPL1 ENST00000294258 52.10 37.02 42.86 0.59 0.77 0.68 1.82 1.68 2.00
CPSF3L ENST00000540437 52.10 54.23 52.47 0.59 0.62 0.61 1.83 1.70 1.92
TCTA ENST00000273590 52.11 89.11 73.41 0.59 0.27 0.42 1.83 0.35 0.77
FGF23 ENST00000237837 52.12 68.99 61.21 0.59 0.54 0.43 1.83 1.15 1.49
C6orf203 ENST00000443043 52.12 70.15 61.88 0.59 0.53 0.47 1.83 1.12 1.45
FAM50B ENST00000380274 52.13 32.59 40.55 0.58 0.86 0.80 1.84 1.47 2.04
DFNB31 ENST00000362057 52.13 33.41 40.99 0.58 0.84 0.76 1.84 1.52 2.05
THNSL2 ENST00000324166 52.14 55.83 53.39 0.59 0.52 0.62 1.84 1.58 1.84
KIAA0141 ENST00000432126 52.14 72.19 63.27 0.59 0.52 0.49 1.84 1.04 1.36
NDUFA2 ENST00000252102 52.15 32.90 40.69 0.59 0.82 0.81 1.84 1.44 2.04
CRYGD ENST00000264376 52.15 78.17 66.88 0.59 0.43 0.53 1.84 0.73 1.20
ACACB ENST00000338432 52.16 44.43 47.03 0.59 0.62 0.70 1.83 1.97 1.89
PNMA1 ENST00000316836 52.16 44.66 47.16 0.59 0.66 0.67 1.83 1.98 1.89
FBXO39 ENST00000321535 52.17 56.44 53.72 0.59 0.52 0.62 1.83 1.54 1.80

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