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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
GAB3 ENST00000424127 22.09 15.21 16.47 1.47 1.89 1.70 1.03 0.67 0.69
SLC23A1 ENST00000353963 22.09 26.10 22.24 1.48 1.20 1.16 1.03 1.09 0.96
SNCA ENST00000394986 22.10 19.34 18.75 1.48 1.48 1.57 1.03 0.74 0.83
TPH2 ENST00000333850 22.10 44.13 31.35 1.48 0.61 0.87 1.04 1.97 1.55
BAZ2B ENST00000392783 22.11 11.82 14.70 1.48 2.09 1.96 1.04 0.57 0.61
SCFD1 ENST00000458591 22.11 7.94 12.58 1.48 2.54 2.20 1.03 0.44 0.52
ATAD5 ENST00000321990 22.12 4.69 11.04 1.48 3.27 2.19 1.03 0.31 0.44
GRIK1 ENST00000399907 22.12 37.39 27.89 1.48 0.76 0.85 1.03 1.66 1.29
ZBTB11 ENST00000312938 22.13 27.24 22.82 1.48 1.25 1.19 1.03 1.15 0.98
CLCF1 ENST00000312438 22.13 13.53 15.68 1.48 2.06 1.76 1.03 0.61 0.67
LIMK1 ENST00000336180 22.14 7.55 12.41 1.48 2.51 2.23 1.04 0.42 0.50
CYTH2 ENST00000452733 22.14 22.95 20.69 1.48 1.47 1.47 1.04 0.90 0.88
WDR7 ENST00000254442 22.15 4.87 11.15 1.49 3.27 2.19 1.04 0.31 0.45
GSKIP ENST00000556095 22.15 52.58 35.52 1.49 0.67 0.85 1.04 1.82 1.78
KIRREL ENST00000359209 22.16 9.62 13.51 1.49 2.48 2.05 1.04 0.50 0.57
S100A10 ENST00000368811 22.16 85.32 53.16 1.49 0.25 0.61 1.04 0.45 1.87
PDZD8 ENST00000334464 22.17 6.47 11.93 1.49 2.62 2.28 1.03 0.37 0.46
POU4F3 ENST00000230732 22.17 16.17 17.03 1.49 1.81 1.67 1.03 0.69 0.70
CRY2 ENST00000443527 22.18 30.92 24.63 1.49 1.05 1.06 1.03 1.36 1.10
PPP4R1 ENST00000400556 22.18 9.11 13.28 1.49 2.47 2.06 1.03 0.47 0.54
KIAA0368 ENST00000259335 22.19 5.17 11.37 1.48 3.19 2.21 1.03 0.32 0.45
BARHL1 ENST00000263610 22.19 39.40 28.96 1.48 0.70 0.81 1.03 1.64 1.31
SLC6A4 ENST00000401766 22.20 20.29 19.21 1.48 1.44 1.54 1.03 0.75 0.86
OSBPL2 ENST00000313733 22.20 23.70 21.10 1.48 1.39 1.42 1.03 0.93 0.90
RELA ENST00000406246 22.21 4.83 11.20 1.48 3.28 2.15 1.03 0.31 0.45

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