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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
PRAMEF12 ENST00000357726 99.43 70.00 87.82 0.11 0.53 0.24 0.12 1.14 0.32
DEFB132 ENST00000382376 99.44 96.88 99.57 0.11 0.23 0.12 0.12 0.19 0.05
FAM153C ENST00000507848 99.44 62.37 84.19 0.11 0.53 0.34 0.12 1.33 0.42
TAS2R50 ENST00000506868 99.45 98.04 99.82 0.11 0.20 0.12 0.12 0.16 0.04
CD300LF ENST00000326165 99.45 76.11 90.86 0.11 0.43 0.15 0.12 0.86 0.20
APOL4 ENST00000352371 99.46 82.85 93.93 0.11 0.32 0.09 0.13 0.49 0.11
ZG16B ENST00000382280 99.46 91.04 97.80 0.11 0.25 0.09 0.13 0.36 0.04
SMCP ENST00000368765 99.47 99.18 99.95 0.11 0.15 0.13 0.13 0.14 0.04
PAGE5 ENST00000289619 99.47 72.11 88.93 0.11 0.52 0.19 0.13 1.04 0.28
TAS2R1 ENST00000382492 99.48 97.80 99.78 0.11 0.21 0.12 0.13 0.18 0.04
RP11-429E11.3 ENST00000317652 99.48 97.57 99.70 0.11 0.22 0.12 0.13 0.20 0.04
TXNDC2 ENST00000306084 99.49 57.21 81.73 0.11 0.56 0.35 0.13 1.49 0.47
ZNF121 ENST00000320451 99.49 86.99 95.97 0.11 0.22 0.07 0.13 0.40 0.10
SCGB2A2 ENST00000227918 99.50 93.88 98.75 0.11 0.25 0.10 0.13 0.26 0.05
C20orf197 ENST00000313426 99.50 85.23 95.10 0.12 0.25 0.09 0.13 0.45 0.10
TGOLN2 ENST00000409232 99.51 39.00 71.82 0.12 0.70 0.44 0.13 1.65 0.82
SCGB1A1 ENST00000278282 99.51 96.14 99.39 0.12 0.21 0.11 0.13 0.20 0.04
PRSS42 ENST00000429665 99.52 74.62 90.13 0.12 0.54 0.18 0.13 0.99 0.21
PLA2G2A ENST00000375111 99.52 68.84 87.38 0.12 0.53 0.28 0.13 1.19 0.31
SLC6A16 ENST00000335875 99.53 60.23 83.25 0.12 0.53 0.29 0.13 1.38 0.40
CXorf66 ENST00000370540 99.54 91.79 98.07 0.12 0.23 0.09 0.13 0.32 0.05
SPN ENST00000360121 99.54 95.92 99.34 0.12 0.22 0.11 0.13 0.20 0.04
TNFRSF10B ENST00000276431 99.55 46.75 76.22 0.12 0.72 0.37 0.13 1.97 0.62
C22orf24 ENST00000248984 99.55 88.55 96.88 0.12 0.24 0.08 0.13 0.36 0.07
CXorf27 ENST00000341016 99.56 99.69 99.99 0.12 0.17 0.13 0.13 0.11 0.04

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