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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
PHLDA1 ENST00000266671 58.76 21.24 38.30 0.56 1.42 0.85 1.50 0.81 2.04
RRP1B ENST00000340648 58.76 44.69 50.79 0.56 0.66 0.67 1.50 1.97 1.85
C15orf38-AP3S2 ENST00000398333 58.77 73.55 68.15 0.56 0.53 0.49 1.49 1.03 1.08
REP15 ENST00000310791 58.77 87.76 76.36 0.56 0.24 0.35 1.49 0.37 0.61
ZNF572 ENST00000319286 58.78 37.23 46.70 0.56 0.77 0.66 1.48 1.66 1.86
ABCB9 ENST00000542678 58.78 33.43 44.68 0.56 0.84 0.62 1.48 1.52 2.06
PCDHGB1 ENST00000523390 58.79 37.74 47.00 0.56 0.80 0.70 1.48 1.70 1.87
ACER1 ENST00000301452 58.79 55.95 57.27 0.56 0.49 0.52 1.48 1.56 1.70
RPAIN ENST00000405578 58.80 91.30 78.31 0.56 0.23 0.38 1.48 0.34 0.54
CGN ENST00000271636 58.80 54.08 56.19 0.56 0.65 0.49 1.48 1.68 1.77
SLC39A12 ENST00000377369 58.81 40.90 48.73 0.56 0.61 0.68 1.48 1.78 1.85
FGF6 ENST00000228837 58.81 77.44 70.45 0.56 0.42 0.43 1.48 0.76 0.91
LTB4R ENST00000396789 58.82 66.50 63.93 0.57 0.57 0.51 1.48 1.22 1.38
EN2 ENST00000297375 58.82 32.88 44.32 0.57 0.82 0.61 1.48 1.44 2.04
MIA ENST00000263369 58.83 80.19 72.15 0.57 0.37 0.43 1.48 0.59 0.82
LIPK ENST00000404190 58.83 55.54 57.07 0.57 0.56 0.52 1.48 1.61 1.71
EMID1 ENST00000334018 58.84 52.14 55.08 0.57 0.62 0.51 1.48 1.85 1.73
TNNI3K ENST00000370891 58.85 76.27 69.78 0.57 0.43 0.44 1.48 0.86 0.93
MANBAL ENST00000373605 58.85 89.54 77.39 0.57 0.27 0.35 1.48 0.36 0.58
HPS6 ENST00000299238 58.86 38.86 47.67 0.57 0.70 0.66 1.48 1.65 1.88
BCHE ENST00000264381 58.86 70.51 66.40 0.57 0.52 0.52 1.48 1.08 1.20
OR1E1 ENST00000322608 58.87 76.99 70.17 0.57 0.43 0.43 1.48 0.78 0.91
RPS6KA6 ENST00000262752 58.87 12.47 33.83 0.57 2.07 0.89 1.48 0.59 1.73
KCNK16 ENST00000425054 58.88 78.80 71.32 0.57 0.42 0.43 1.48 0.71 0.87
BEND4 ENST00000502486 58.88 12.54 33.88 0.58 2.09 0.89 1.48 0.58 1.73

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