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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
OR51A4 ENST00000380373 84.84 94.93 92.63 0.28 0.23 0.14 0.46 0.23 0.15
MID1IP1 ENST00000336949 84.85 62.96 77.06 0.28 0.51 0.37 0.46 1.31 0.61
GYPC ENST00000259254 84.85 67.32 79.37 0.28 0.56 0.39 0.46 1.20 0.52
ACSBG2 ENST00000586696 84.86 48.72 68.79 0.28 0.63 0.46 0.46 1.99 1.05
SPDYE4 ENST00000328794 84.86 46.32 67.39 0.28 0.73 0.52 0.46 2.03 1.15
RP11-113D6.10 ENST00000340135 84.87 90.10 90.55 0.28 0.25 0.15 0.46 0.37 0.21
ZCCHC5 ENST00000321110 84.87 92.95 91.74 0.28 0.29 0.14 0.46 0.30 0.18
CLEC4D ENST00000299665 84.88 82.81 87.04 0.28 0.32 0.28 0.46 0.50 0.30
CGB1 ENST00000301407 84.88 88.85 89.95 0.28 0.25 0.18 0.46 0.35 0.23
TAS2R3 ENST00000247879 84.89 87.89 89.52 0.28 0.24 0.18 0.46 0.38 0.23
XAF1 ENST00000361842 84.89 86.83 88.96 0.28 0.23 0.19 0.46 0.40 0.28
SERPINA1 ENST00000448921 84.90 86.20 88.67 0.28 0.27 0.20 0.46 0.42 0.28
C2orf27A ENST00000355171 84.90 89.64 90.32 0.28 0.27 0.15 0.46 0.36 0.21
MROH9 ENST00000367759 84.91 53.66 71.89 0.28 0.63 0.44 0.46 1.70 0.82
OXT ENST00000217386 84.91 38.79 62.81 0.28 0.70 0.48 0.46 1.66 1.39
PLEKHJ1 ENST00000589097 84.92 56.73 73.61 0.28 0.53 0.40 0.46 1.56 0.74
CTU2 ENST00000453996 84.92 78.22 84.92 0.28 0.43 0.34 0.46 0.74 0.40
COA6 ENST00000366613 84.93 76.42 83.97 0.28 0.44 0.35 0.46 0.85 0.43
OR8B2 ENST00000375013 84.93 95.23 92.84 0.28 0.23 0.14 0.46 0.21 0.15
UPK3BL ENST00000340457 84.94 92.34 91.51 0.28 0.25 0.15 0.46 0.30 0.18
BTN2A1 ENST00000312541 84.94 92.82 91.70 0.28 0.29 0.14 0.46 0.30 0.18
CHADL ENST00000216241 84.95 65.01 78.24 0.28 0.51 0.37 0.46 1.24 0.55
TP53I13 ENST00000301057 84.95 52.22 70.98 0.28 0.62 0.43 0.46 1.84 0.85
OR51H1P ENST00000322059 84.96 66.75 79.18 0.28 0.56 0.38 0.46 1.22 0.54
IQCE ENST00000402050 84.96 82.43 86.86 0.28 0.34 0.29 0.46 0.52 0.31

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