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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
HDAC4 ENST00000345617 13.48 0.13 4.10 1.66 4.12 3.76 0.68 0.28 0.23
PRKDC ENST00000314191 43.22 0.14 19.69 0.82 4.11 1.53 1.80 0.28 0.85
SMG1 ENST00000446231 14.23 0.14 4.48 1.61 4.13 3.70 0.73 0.28 0.25
COL5A1 ENST00000371817 35.81 0.15 15.80 0.95 4.13 1.77 1.89 0.28 0.66
NBEA ENST00000400445 17.84 0.15 6.32 1.52 4.13 3.11 0.90 0.28 0.32
SYNGAP1 ENST00000418600 4.15 0.16 0.66 3.72 4.12 4.63 0.30 0.28 0.20
SMARCA4 ENST00000429416 0.95 0.17 0.04 4.38 4.12 4.88 0.18 0.28 0.15
MED12 ENST00000374080 3.80 0.17 0.58 3.77 4.11 4.70 0.30 0.28 0.17
AGO1 ENST00000373204 1.93 0.18 0.17 4.28 4.11 4.87 0.24 0.28 0.18
SCN1A ENST00000303395 3.07 0.18 0.41 3.87 4.13 4.77 0.30 0.28 0.17
TNPO1 ENST00000337273 2.61 0.19 0.30 4.03 4.15 4.85 0.28 0.28 0.18
ARID1A ENST00000324856 13.75 0.19 4.26 1.64 4.15 3.76 0.69 0.28 0.24
ZC3H4 ENST00000253048 44.50 0.20 20.45 0.63 4.14 1.49 1.78 0.28 0.89
GREB1L ENST00000580732 15.17 0.20 4.97 1.56 4.14 3.70 0.76 0.28 0.25
KDM3B ENST00000314358 2.20 0.21 0.24 4.19 4.13 4.83 0.28 0.28 0.18
KMT2B ENST00000222270 3.06 0.21 0.42 3.88 4.13 4.77 0.30 0.28 0.17
ARHGAP35 ENST00000404338 6.63 0.22 1.44 2.97 4.13 4.33 0.37 0.28 0.23
TOP1 ENST00000361337 0.69 0.22 0.03 4.34 4.12 4.88 0.19 0.28 0.15
LRP1 ENST00000243077 10.60 0.23 2.83 1.99 4.12 4.03 0.57 0.28 0.23
GRIN2B ENST00000609686 0.49 0.23 0.02 4.40 4.11 4.89 0.18 0.28 0.15
KMT2E ENST00000311117 19.13 0.24 7.03 1.58 4.11 2.90 0.95 0.28 0.33
SPEN ENST00000375759 15.99 0.24 5.45 1.53 4.13 3.44 0.79 0.28 0.26
HUWE1 ENST00000342160 4.81 0.25 0.86 3.60 4.12 4.51 0.30 0.28 0.20
ASH1L ENST00000392403 12.67 0.25 3.83 1.68 4.12 3.77 0.66 0.28 0.24
UBTF ENST00000302904 1.80 0.26 0.16 4.28 4.12 4.86 0.22 0.28 0.18

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