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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
WBP2NL ENST00000328823 85.74 82.35 87.22 0.27 0.34 0.28 0.45 0.52 0.31
CGB7 ENST00000597853 85.75 94.30 92.77 0.27 0.24 0.14 0.45 0.25 0.15
FAAH2 ENST00000374900 85.75 96.45 93.86 0.27 0.22 0.10 0.45 0.19 0.12
IGLL1 ENST00000330377 85.76 77.83 85.11 0.27 0.42 0.33 0.45 0.79 0.38
UFSP1 ENST00000388761 85.77 91.92 91.66 0.27 0.23 0.14 0.45 0.32 0.18
OR5AK2 ENST00000326855 85.77 86.19 89.10 0.27 0.27 0.19 0.45 0.42 0.26
C9orf96 ENST00000371957 85.78 73.13 82.84 0.27 0.53 0.32 0.45 1.02 0.42
IBSP ENST00000226284 85.78 78.68 85.59 0.27 0.40 0.32 0.45 0.74 0.35
SSC5D ENST00000389623 85.79 62.78 77.50 0.27 0.51 0.35 0.45 1.31 0.57
CYP26C1 ENST00000285949 85.79 46.87 68.30 0.27 0.71 0.51 0.45 1.96 1.07
MYL5 ENST00000400159 85.80 96.92 94.10 0.27 0.23 0.09 0.45 0.19 0.12
RP11-683L23.1 ENST00000308911 85.80 92.67 91.98 0.27 0.29 0.14 0.45 0.31 0.16
PATE2 ENST00000358524 85.81 86.58 89.31 0.27 0.24 0.18 0.45 0.41 0.25
SAMD11 ENST00000342066 85.81 62.46 77.27 0.27 0.53 0.35 0.45 1.31 0.58
CPZ ENST00000360986 85.82 97.19 94.24 0.27 0.24 0.10 0.45 0.19 0.12
MRPS34 ENST00000397375 85.82 87.05 89.55 0.27 0.22 0.18 0.45 0.40 0.23
C1orf115 ENST00000294889 85.83 88.50 90.21 0.27 0.23 0.18 0.45 0.36 0.21
KRTAP4-16P ENST00000440582 85.83 99.83 95.63 0.27 0.17 0.08 0.45 0.11 0.11
COMT ENST00000361682 85.84 81.50 86.83 0.27 0.33 0.29 0.45 0.54 0.32
DCAF8L2 ENST00000451261 85.84 24.19 54.60 0.27 1.33 0.56 0.45 0.98 1.74
OR4C15 ENST00000314644 85.85 96.95 94.16 0.27 0.24 0.09 0.45 0.19 0.12
REG1B ENST00000305089 85.85 83.85 88.01 0.27 0.28 0.24 0.45 0.47 0.31
ISG15 ENST00000379389 85.86 87.25 89.66 0.27 0.22 0.18 0.45 0.41 0.23
SLFN5 ENST00000299977 85.86 73.41 82.98 0.27 0.54 0.32 0.45 1.03 0.40
IFNA8 ENST00000380205 85.87 99.08 95.03 0.27 0.15 0.09 0.45 0.14 0.10

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