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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
BST2 ENST00000252593 99.87 74.66 90.29 0.12 0.54 0.15 0.14 0.97 0.21
VN1R1 ENST00000321039 99.87 98.22 99.90 0.12 0.21 0.12 0.14 0.15 0.04
MUC7 ENST00000413702 99.86 95.76 99.38 0.12 0.23 0.11 0.13 0.20 0.04
IL31 ENST00000377035 99.86 85.94 95.66 0.12 0.28 0.07 0.13 0.43 0.11
BPIFA2 ENST00000253362 99.85 80.21 92.78 0.12 0.37 0.14 0.13 0.59 0.15
ANXA2R ENST00000314890 99.85 98.39 100.00 0.12 0.21 0.13 0.13 0.14 0.04
APOL6 ENST00000409652 99.84 93.93 98.87 0.12 0.25 0.10 0.13 0.26 0.05
CD209 ENST00000315599 99.83 72.43 89.24 0.12 0.49 0.19 0.13 1.03 0.25
ZNF268 ENST00000536435 99.83 48.55 77.39 0.12 0.65 0.35 0.13 2.01 0.58
RARRES3 ENST00000255688 99.82 94.70 99.10 0.12 0.23 0.11 0.13 0.24 0.04
IL3 ENST00000296870 99.82 95.99 99.44 0.12 0.22 0.11 0.13 0.20 0.05
CCL15 ENST00000354059 99.81 59.99 83.27 0.12 0.53 0.30 0.13 1.37 0.40
CCL1 ENST00000225842 99.81 89.41 97.29 0.12 0.27 0.08 0.13 0.37 0.07
TMEM225 ENST00000375026 99.80 76.04 90.96 0.12 0.43 0.15 0.13 0.86 0.20
ZNF823 ENST00000341191 99.80 55.75 81.13 0.12 0.52 0.39 0.13 1.59 0.49
C17orf102 ENST00000357754 99.79 91.09 97.93 0.12 0.25 0.09 0.13 0.35 0.04
KIF25 ENST00000443060 99.79 69.30 87.69 0.12 0.57 0.24 0.13 1.14 0.31
IGFL4 ENST00000377697 99.78 79.94 92.61 0.12 0.37 0.14 0.13 0.61 0.15
ZNF589 ENST00000354698 99.78 80.97 93.13 0.12 0.35 0.14 0.13 0.57 0.15
AC106876.2 ENST00000409905 99.77 87.30 96.28 0.12 0.22 0.07 0.13 0.41 0.09
SPANXN3 ENST00000370503 99.77 87.33 96.29 0.12 0.22 0.07 0.13 0.41 0.09
LRRC25 ENST00000339007 99.76 19.70 60.18 0.12 1.43 0.48 0.13 0.74 1.61
IGSF23 ENST00000402988 99.76 70.20 88.13 0.12 0.53 0.23 0.13 1.12 0.30
CLEC4M ENST00000327325 99.75 62.08 84.21 0.12 0.56 0.34 0.13 1.36 0.42
CD2 ENST00000369478 99.75 34.49 69.22 0.12 0.80 0.44 0.13 1.56 0.98

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