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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
ULBP2 ENST00000367351 98.92 92.56 98.11 0.10 0.29 0.09 0.11 0.31 0.05
C9orf47 ENST00000334490 98.92 88.39 96.42 0.10 0.23 0.07 0.11 0.37 0.09
PRH2 ENST00000396400 98.93 78.42 91.54 0.10 0.43 0.15 0.11 0.73 0.18
DEFB112 ENST00000322246 98.93 94.06 98.63 0.10 0.25 0.10 0.11 0.26 0.05
PODXL ENST00000378555 98.94 37.08 70.31 0.10 0.78 0.43 0.11 1.66 0.91
CARD18 ENST00000530950 98.94 91.72 97.87 0.10 0.24 0.09 0.11 0.32 0.04
OR2M2 ENST00000359682 98.95 97.67 99.62 0.10 0.21 0.12 0.11 0.19 0.04
C2orf48 ENST00000381786 98.95 69.59 87.43 0.10 0.52 0.28 0.11 1.10 0.31
SLFN12 ENST00000394562 98.96 72.76 88.98 0.10 0.48 0.19 0.11 1.04 0.28
TREM1 ENST00000244709 98.96 54.79 80.21 0.10 0.57 0.35 0.11 1.63 0.52
ZNF845 ENST00000458035 98.97 94.39 98.74 0.10 0.23 0.10 0.11 0.24 0.05
FLJ45079 ENST00000374983 98.97 98.21 99.77 0.10 0.21 0.12 0.12 0.15 0.04
C3orf27 ENST00000356020 98.98 97.56 99.60 0.11 0.22 0.12 0.12 0.19 0.05
C4orf3 ENST00000399075 98.98 44.42 74.62 0.11 0.61 0.40 0.12 1.97 0.68
POM121L2 ENST00000444565 98.99 91.08 97.62 0.11 0.25 0.09 0.12 0.36 0.06
MAP7D3 ENST00000316077 98.99 54.56 80.09 0.11 0.59 0.35 0.12 1.66 0.52
MUCL1 ENST00000308796 99.00 94.64 98.85 0.11 0.23 0.10 0.12 0.24 0.05
GYPA ENST00000360771 99.00 65.12 85.41 0.11 0.49 0.34 0.12 1.24 0.35
C11orf34 ENST00000338832 99.01 85.57 95.05 0.11 0.27 0.09 0.12 0.44 0.10
KIAA0947 ENST00000296564 99.01 3.70 50.40 0.11 3.33 0.67 0.12 0.30 1.90
PRAP1 ENST00000433452 99.02 68.81 87.10 0.11 0.53 0.28 0.12 1.19 0.30
LAIR1 ENST00000391742 99.02 67.54 86.46 0.11 0.53 0.30 0.12 1.20 0.33
HJURP ENST00000411486 99.03 43.26 73.93 0.11 0.61 0.40 0.12 1.92 0.70
MAGEB4 ENST00000378982 99.03 97.73 99.66 0.11 0.21 0.12 0.12 0.17 0.04
SECTM1 ENST00000269389 99.04 62.25 83.93 0.11 0.53 0.35 0.12 1.34 0.43

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