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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
CEACAM18 ENST00000451626 99.16 87.46 96.04 0.11 0.23 0.07 0.12 0.40 0.11
CTAGE15 ENST00000420911 88.66 97.86 96.05 0.19 0.21 0.07 0.34 0.17 0.11
VCX3B ENST00000381032 95.92 90.70 96.05 0.11 0.25 0.07 0.11 0.35 0.11
TPSG1 ENST00000234798 89.49 97.12 96.06 0.16 0.24 0.07 0.30 0.18 0.11
SFT2D3 ENST00000310981 91.34 93.46 96.06 0.15 0.28 0.07 0.20 0.28 0.11
AC137932.1 ENST00000602042 91.43 94.80 96.07 0.15 0.23 0.07 0.20 0.24 0.11
LGALS16 ENST00000392051 98.78 87.88 96.07 0.10 0.24 0.07 0.11 0.38 0.11
SPAG11B ENST00000398462 95.03 91.65 96.08 0.10 0.24 0.07 0.12 0.32 0.11
CPXCR1 ENST00000276127 88.92 97.70 96.08 0.19 0.21 0.07 0.32 0.18 0.11
CTD-3203P2.2 ENST00000566854 94.27 92.44 96.09 0.10 0.27 0.07 0.12 0.30 0.11
AL391421.1 ENST00000372387 91.38 94.91 96.10 0.15 0.23 0.07 0.20 0.23 0.11
TRIM49D1 ENST00000530311 92.78 93.62 96.10 0.15 0.28 0.07 0.17 0.28 0.11
ZNF587B ENST00000442832 97.46 89.26 96.11 0.10 0.27 0.07 0.11 0.36 0.10
RP11-268J15.5 ENST00000373137 86.88 99.80 96.11 0.24 0.17 0.07 0.40 0.11 0.10
NUPR1L ENST00000329309 91.62 96.33 96.12 0.15 0.22 0.07 0.20 0.19 0.10
C9orf16 ENST00000372994 91.20 95.09 96.12 0.15 0.23 0.07 0.21 0.21 0.10
RP11-15E18.4 ENST00000592917 90.98 95.33 96.13 0.16 0.24 0.07 0.21 0.21 0.10
RBMY1J ENST00000250831 92.69 93.73 96.13 0.15 0.28 0.07 0.17 0.26 0.10
LCE3B ENST00000335633 90.01 95.08 96.14 0.16 0.23 0.07 0.26 0.21 0.10
NAT8 ENST00000272425 88.12 98.48 96.14 0.20 0.21 0.07 0.35 0.15 0.10
IL3RA ENST00000331035 95.58 91.28 96.15 0.11 0.23 0.07 0.11 0.34 0.10
NUTM2E ENST00000429984 90.48 96.04 96.15 0.16 0.21 0.07 0.25 0.20 0.10
GOLGA8S ENST00000562295 89.50 97.36 96.16 0.16 0.22 0.07 0.30 0.19 0.10
ZNF717 ENST00000422325 93.41 95.55 96.16 0.13 0.23 0.07 0.15 0.21 0.10
SPRR2G ENST00000368748 88.62 99.05 96.17 0.20 0.15 0.07 0.34 0.14 0.10

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