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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
UBR7 ENST00000013070 6.52 21.58 11.68 3.02 1.44 2.23 0.37 0.81 0.47
MAP4K5 ENST00000013125 27.41 8.57 15.81 1.21 2.51 1.77 1.41 0.47 0.66
INMT ENST00000013222 84.00 85.90 88.09 0.30 0.28 0.23 0.48 0.43 0.30
ERCC1 ENST00000013807 32.27 69.75 50.00 0.97 0.53 0.62 1.70 1.13 1.90
GPRC5A ENST00000014914 71.91 84.52 81.59 0.33 0.29 0.37 0.81 0.43 0.47
HEBP1 ENST00000014930 61.54 84.84 76.28 0.68 0.27 0.37 1.31 0.42 0.62
COX15 ENST00000016171 36.06 70.22 52.41 0.94 0.52 0.61 1.84 1.12 1.91
MS4A12 ENST00000016913 95.29 88.31 94.54 0.10 0.23 0.10 0.11 0.37 0.12
XYLT2 ENST00000017003 26.34 15.94 19.13 1.32 1.87 1.53 1.27 0.68 0.85
SCTR ENST00000019103 57.40 60.63 59.21 0.57 0.53 0.49 1.55 1.41 1.68
RALBP1 ENST00000019317 8.31 21.79 12.61 2.54 1.46 2.20 0.44 0.81 0.52
PSD ENST00000020673 22.33 14.72 16.35 1.46 1.97 1.71 1.06 0.62 0.67
SYT13 ENST00000020926 48.11 22.67 33.54 0.54 1.46 0.89 1.78 0.88 1.72
SLC7A9 ENST00000023064 58.94 61.61 60.87 0.56 0.54 0.43 1.48 1.41 1.60
RTFDC1 ENST00000023939 22.82 44.00 31.62 1.44 0.61 0.89 1.05 1.97 1.57
SLC45A4 ENST00000024061 54.89 36.94 44.42 0.63 0.75 0.61 1.71 1.70 2.04
RB1CC1 ENST00000025008 24.49 2.56 11.17 1.34 3.55 2.18 1.12 0.29 0.45
AKAP11 ENST00000025301 32.05 11.88 19.99 0.97 2.10 1.47 1.72 0.58 0.85
PIGQ ENST00000026218 71.93 46.19 59.28 0.33 0.73 0.51 0.81 2.03 1.68
CDH17 ENST00000027335 61.99 52.79 57.29 0.71 0.65 0.51 1.29 1.80 1.68
B4GALT7 ENST00000029410 63.86 64.56 65.82 0.58 0.48 0.51 1.22 1.21 1.25
FAM13B ENST00000033079 20.03 15.12 15.34 1.53 1.91 1.80 1.00 0.66 0.66
CHPF2 ENST00000035307 65.05 65.44 66.99 0.54 0.53 0.53 1.17 1.25 1.19
LRRC7 ENST00000035383 1.64 2.52 0.62 4.29 3.57 4.66 0.22 0.29 0.19
GABARAPL2 ENST00000037243 12.80 82.39 46.25 1.68 0.34 0.67 0.66 0.52 1.93

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