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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
SMCR8 ENST00000406438 48.69 34.29 39.83 0.51 0.85 0.78 1.83 1.56 2.03
TBX2 ENST00000240328 48.69 9.53 27.25 0.51 2.51 0.99 1.82 0.49 1.25
NEUROD4 ENST00000242994 48.70 53.68 50.19 0.51 0.63 0.63 1.82 1.69 1.90
DNAH1 ENST00000420323 48.70 23.34 34.30 0.51 1.42 0.87 1.82 0.93 1.77
CLUH ENST00000570628 48.71 11.56 28.31 0.51 2.10 0.78 1.82 0.57 1.29
OR4D2 ENST00000545221 48.71 81.95 67.07 0.51 0.35 0.51 1.82 0.51 1.16
SLC4A9 ENST00000230993 48.72 60.16 53.89 0.52 0.52 0.61 1.82 1.38 1.78
SLC28A2 ENST00000347644 48.72 78.93 65.33 0.52 0.40 0.53 1.82 0.69 1.32
TRIM56 ENST00000306085 48.73 47.97 47.08 0.52 0.61 0.68 1.82 2.00 1.88
ANKMY2 ENST00000306999 48.73 48.11 47.18 0.52 0.63 0.67 1.82 1.99 1.89
IL18 ENST00000280357 48.74 72.39 61.18 0.52 0.51 0.43 1.82 1.03 1.50
FAM19A4 ENST00000295569 48.74 61.40 54.65 0.52 0.54 0.56 1.82 1.40 1.73
TTC21A ENST00000431162 48.75 50.98 48.74 0.52 0.65 0.68 1.82 1.92 1.85
LARS2 ENST00000415258 48.75 44.73 45.45 0.52 0.66 0.70 1.82 1.98 1.99
PREB ENST00000260643 48.76 41.18 43.32 0.52 0.59 0.63 1.82 1.82 2.00
SNED1 ENST00000310397 48.76 14.46 29.78 0.52 2.04 0.86 1.82 0.61 1.43
DOK1 ENST00000233668 48.77 34.04 39.76 0.52 0.82 0.80 1.82 1.55 2.04
CCDC41 ENST00000397809 48.77 48.77 47.53 0.52 0.63 0.63 1.83 2.01 1.89
FAM26D ENST00000405399 48.78 85.67 69.36 0.52 0.27 0.43 1.83 0.44 0.98
CDK15 ENST00000450471 48.78 74.93 62.82 0.52 0.53 0.48 1.83 0.94 1.39
SRP19 ENST00000505459 48.79 53.08 49.90 0.52 0.66 0.63 1.82 1.77 1.89
ASB6 ENST00000277458 48.79 52.82 49.74 0.52 0.65 0.66 1.83 1.80 1.86
AASDH ENST00000205214 48.80 44.91 45.57 0.52 0.68 0.68 1.83 1.99 1.97
SNPH ENST00000381873 48.80 12.67 28.88 0.52 2.10 0.81 1.83 0.58 1.31
WDR72 ENST00000396328 48.81 58.59 53.12 0.52 0.54 0.61 1.83 1.42 1.87

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