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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
RFPL3S ENST00000400234 97.25 74.89 89.18 0.10 0.53 0.19 0.11 0.95 0.25
OR7C1 ENST00000248073 98.45 97.99 99.60 0.10 0.20 0.12 0.11 0.17 0.05
ZNF578 ENST00000421239 96.66 93.53 97.68 0.11 0.28 0.09 0.11 0.28 0.06
PRG2 ENST00000311862 97.85 69.86 87.05 0.11 0.54 0.28 0.11 1.14 0.30
VN1R4 ENST00000311170 96.06 99.15 99.32 0.11 0.15 0.11 0.11 0.14 0.04
CLEC4C ENST00000542353 97.26 72.15 87.81 0.10 0.52 0.24 0.11 1.04 0.32
FMR1NB ENST00000370467 98.45 48.03 76.35 0.10 0.63 0.35 0.11 2.00 0.61
DEFA4 ENST00000297435 96.66 78.59 90.68 0.11 0.40 0.15 0.11 0.74 0.20
ZNF528 ENST00000360465 96.07 81.60 91.65 0.11 0.33 0.14 0.11 0.52 0.18
LACRT ENST00000257867 97.86 87.06 95.17 0.11 0.22 0.09 0.11 0.40 0.10
ZNF836 ENST00000322146 97.26 96.86 99.02 0.10 0.23 0.11 0.11 0.19 0.04
MDS2 ENST00000374555 96.67 60.53 81.98 0.11 0.52 0.37 0.11 1.41 0.47
C7orf69 ENST00000258776 98.46 91.39 97.52 0.10 0.23 0.08 0.11 0.33 0.07
FAM47A ENST00000346193 96.07 97.90 99.18 0.11 0.20 0.11 0.11 0.17 0.04
INSL4 ENST00000239316 97.86 95.54 98.77 0.11 0.23 0.10 0.11 0.21 0.05
GLIPR1L1 ENST00000312442 97.27 76.98 90.18 0.10 0.43 0.18 0.11 0.79 0.21
KHDC1 ENST00000370384 96.67 89.22 95.73 0.11 0.27 0.07 0.11 0.36 0.11
XKR3 ENST00000331428 96.08 51.60 76.96 0.11 0.62 0.37 0.11 1.87 0.61
DPPA3 ENST00000345088 98.46 46.98 75.72 0.10 0.71 0.38 0.11 1.95 0.64
MUC17 ENST00000306151 97.87 77.43 90.71 0.11 0.42 0.15 0.11 0.76 0.20
KLK4 ENST00000324041 97.27 73.92 88.72 0.10 0.53 0.20 0.11 1.02 0.28
DEFB1 ENST00000297439 96.68 89.19 95.71 0.11 0.27 0.07 0.11 0.36 0.11
KRTAP9-8 ENST00000254072 96.08 98.60 99.23 0.11 0.20 0.11 0.11 0.15 0.04
TAS2R8 ENST00000240615 98.47 99.56 99.88 0.10 0.16 0.12 0.11 0.13 0.04
ADM5 ENST00000420022 97.87 88.53 95.94 0.11 0.23 0.07 0.11 0.36 0.10

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