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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
RBMXL2 ENST00000306904 77.74 37.75 57.76 0.34 0.80 0.49 0.67 1.70 1.67
SPRED3 ENST00000338502 77.74 39.65 58.80 0.34 0.68 0.51 0.67 1.65 1.65
SOX7 ENST00000554914 77.75 66.14 74.85 0.34 0.53 0.39 0.67 1.20 0.64
TMEM237 ENST00000409883 77.75 69.18 76.56 0.33 0.56 0.38 0.67 1.12 0.61
PPP1R35 ENST00000292330 77.76 77.02 80.72 0.33 0.43 0.39 0.67 0.78 0.52
C1orf63 ENST00000243189 77.76 88.75 86.45 0.33 0.25 0.30 0.67 0.36 0.32
C14orf166B ENST00000393774 77.77 70.98 77.59 0.33 0.49 0.37 0.67 1.06 0.56
ALG12 ENST00000330817 77.77 56.09 69.00 0.33 0.51 0.46 0.68 1.56 1.03
CD93 ENST00000246006 77.78 64.83 74.14 0.33 0.48 0.39 0.67 1.24 0.69
C7 ENST00000313164 77.79 50.54 65.76 0.33 0.63 0.51 0.67 1.95 1.26
PCNT ENST00000359568 77.79 43.13 61.08 0.33 0.62 0.43 0.67 1.89 1.53
GLTPD1 ENST00000343938 77.80 75.28 79.86 0.32 0.49 0.37 0.67 0.90 0.52
OR52K1 ENST00000307632 77.80 97.20 90.58 0.32 0.24 0.15 0.67 0.19 0.20
GOT1L1 ENST00000307599 77.81 71.39 77.79 0.32 0.53 0.38 0.67 1.05 0.54
PCDHB16 ENST00000361016 77.81 69.28 76.63 0.32 0.57 0.37 0.67 1.14 0.61
TMEM71 ENST00000356838 77.82 77.35 80.92 0.32 0.42 0.39 0.67 0.76 0.51
IL1A ENST00000263339 77.82 73.01 78.68 0.32 0.51 0.38 0.68 1.03 0.54
SLC7A4 ENST00000382932 77.83 69.60 76.86 0.32 0.52 0.35 0.68 1.10 0.61
ZNF790 ENST00000356725 77.83 71.11 77.68 0.32 0.49 0.38 0.67 1.07 0.55
CABS1 ENST00000273936 77.84 72.37 78.35 0.32 0.51 0.38 0.67 1.03 0.54
IL1RL2 ENST00000264257 77.84 54.42 68.07 0.32 0.62 0.51 0.67 1.66 1.10
C12orf43 ENST00000288757 77.85 77.42 80.97 0.32 0.42 0.39 0.67 0.76 0.50
USHBP1 ENST00000252597 77.85 62.17 72.71 0.32 0.53 0.43 0.67 1.35 0.81
HDAC10 ENST00000216271 77.86 80.41 82.55 0.32 0.37 0.32 0.67 0.59 0.43
RP1-241P17.4 ENST00000449327 77.86 95.25 89.68 0.32 0.23 0.18 0.67 0.21 0.23

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