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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
C21orf58 ENST00000291691 95.82 86.02 93.69 0.11 0.25 0.11 0.11 0.43 0.14
APOL5 ENST00000249044 95.82 67.05 84.79 0.11 0.54 0.34 0.11 1.24 0.40
TPRX1 ENST00000322175 95.83 89.38 95.32 0.11 0.27 0.08 0.11 0.37 0.10
IFNA10 ENST00000357374 95.83 98.81 99.20 0.11 0.16 0.11 0.11 0.14 0.04
IFNA14 ENST00000380222 95.84 98.13 98.92 0.11 0.20 0.10 0.11 0.16 0.04
C4orf50 ENST00000531445 95.84 73.17 87.65 0.11 0.53 0.25 0.11 1.02 0.31
PSG5 ENST00000366175 95.85 95.38 98.05 0.11 0.24 0.09 0.11 0.21 0.05
PRAMEF20 ENST00000316412 95.85 95.81 98.21 0.11 0.22 0.09 0.11 0.20 0.05
PATE1 ENST00000305738 95.86 96.70 98.51 0.11 0.23 0.10 0.11 0.19 0.05
AP003774.4 ENST00000316124 95.86 87.03 94.19 0.11 0.22 0.09 0.11 0.40 0.12
C14orf79 ENST00000547315 95.87 89.55 95.48 0.11 0.27 0.08 0.11 0.36 0.11
FAM220A ENST00000313324 95.87 99.14 99.28 0.11 0.15 0.11 0.11 0.14 0.04
RHOXF2B ENST00000371402 95.88 74.21 88.20 0.11 0.53 0.23 0.11 1.02 0.30
SPATA31A3 ENST00000356699 95.88 93.42 97.31 0.11 0.28 0.08 0.11 0.28 0.07
C9orf170 ENST00000375941 95.89 97.04 98.62 0.11 0.24 0.10 0.11 0.19 0.05
PSG8 ENST00000306511 95.89 96.93 98.59 0.11 0.24 0.10 0.11 0.19 0.05
PPBP ENST00000296028 95.90 82.64 92.00 0.11 0.34 0.14 0.11 0.50 0.16
GZMM ENST00000264553 95.90 66.72 84.64 0.11 0.56 0.34 0.11 1.21 0.40
C9orf153 ENST00000376001 95.91 91.62 96.55 0.11 0.23 0.07 0.11 0.32 0.07
ZNF561 ENST00000302851 95.91 85.45 93.40 0.11 0.25 0.11 0.11 0.45 0.15
IL2RA ENST00000379959 95.92 34.72 67.07 0.11 0.77 0.51 0.11 1.54 1.16
VCX3B ENST00000381032 95.92 90.70 96.05 0.11 0.25 0.07 0.11 0.35 0.11
OR5T1 ENST00000313033 95.93 99.96 99.48 0.11 0.18 0.11 0.11 0.09 0.05
C22orf42 ENST00000382097 95.94 89.38 95.41 0.11 0.27 0.08 0.11 0.37 0.11
C13orf35 ENST00000356049 95.94 78.54 90.28 0.11 0.40 0.15 0.11 0.74 0.22

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