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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
HTRA3 ENST00000307358 73.61 64.61 71.69 0.35 0.48 0.44 0.79 1.22 0.82
DLL3 ENST00000205143 73.61 46.88 60.86 0.35 0.71 0.43 0.79 1.95 1.60
TRMT112 ENST00000544844 73.62 64.99 71.90 0.34 0.49 0.43 0.79 1.24 0.81
HIST2H3D ENST00000331491 73.62 95.17 87.53 0.34 0.23 0.28 0.79 0.21 0.30
CECR1 ENST00000399839 73.63 58.62 68.10 0.34 0.54 0.51 0.79 1.42 1.10
MYOZ3 ENST00000297130 73.63 76.01 78.01 0.34 0.43 0.38 0.79 0.86 0.54
ARL14 ENST00000320767 73.64 93.78 86.88 0.34 0.27 0.29 0.79 0.26 0.31
ANKRD2 ENST00000307518 73.64 68.89 74.10 0.34 0.54 0.39 0.79 1.17 0.69
MRPL53 ENST00000258105 73.65 71.72 75.66 0.34 0.51 0.38 0.79 1.07 0.64
MRPS2 ENST00000371785 73.65 92.09 86.10 0.34 0.24 0.33 0.79 0.32 0.33
RDH13 ENST00000415061 73.66 89.87 85.10 0.34 0.27 0.33 0.79 0.37 0.38
ALDH3B1 ENST00000539229 73.66 54.34 65.53 0.34 0.62 0.52 0.79 1.68 1.29
COL21A1 ENST00000244728 73.67 52.32 64.28 0.34 0.62 0.51 0.79 1.82 1.35
ISG20 ENST00000306072 73.67 85.72 83.04 0.34 0.27 0.30 0.80 0.44 0.40
UGT1A4 ENST00000373409 73.68 64.05 71.35 0.34 0.49 0.43 0.80 1.21 0.87
B3GAT2 ENST00000230053 73.68 75.60 77.84 0.34 0.44 0.38 0.80 0.90 0.54
NNMT ENST00000535401 73.69 91.67 85.95 0.34 0.24 0.33 0.80 0.32 0.33
LRTM1 ENST00000273286 73.69 92.46 86.30 0.34 0.27 0.33 0.80 0.30 0.33
BTNL2 ENST00000454136 73.70 71.13 75.33 0.34 0.51 0.37 0.81 1.07 0.65
C16orf58 ENST00000327237 73.70 78.12 79.24 0.34 0.43 0.38 0.81 0.74 0.54
SPRY3 ENST00000302805 73.71 64.74 71.78 0.34 0.48 0.46 0.81 1.24 0.81
DNASE1L1 ENST00000369809 73.72 39.72 56.53 0.34 0.66 0.52 0.81 1.66 1.70
DTYMK ENST00000305784 73.72 80.21 80.29 0.34 0.37 0.38 0.81 0.59 0.52
CRISPLD2 ENST00000262424 73.73 44.97 59.68 0.34 0.68 0.49 0.80 1.97 1.67
PCDHB15 ENST00000231173 73.73 72.15 75.96 0.34 0.52 0.38 0.80 1.04 0.62

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