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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
AC003101.1 ENST00000412403 94.43 92.54 96.22 0.10 0.29 0.07 0.11 0.31 0.09
SMIM22 ENST00000589327 93.58 95.79 96.22 0.13 0.22 0.07 0.14 0.20 0.09
NBPF20 ENST00000369202 89.59 97.39 96.21 0.16 0.22 0.07 0.30 0.19 0.10
RP11-272B17.2 ENST00000548613 89.90 96.94 96.21 0.18 0.24 0.07 0.28 0.19 0.10
KRTAP15-1 ENST00000334067 87.61 99.99 96.20 0.23 0.18 0.07 0.37 0.09 0.10
HEPN1 ENST00000408930 87.35 99.51 96.20 0.23 0.16 0.07 0.38 0.13 0.10
PSG9 ENST00000270077 95.13 91.80 96.19 0.10 0.23 0.07 0.12 0.32 0.10
FAM163B ENST00000496132 94.03 93.64 96.19 0.10 0.28 0.07 0.13 0.28 0.10
RP11-625H11.1 ENST00000558940 95.81 91.10 96.18 0.11 0.25 0.07 0.11 0.35 0.10
OCLM ENST00000574641 88.06 98.29 96.18 0.20 0.21 0.07 0.35 0.15 0.10
OR5A2 ENST00000302040 88.95 97.84 96.17 0.19 0.21 0.07 0.32 0.17 0.10
SPRR2G ENST00000368748 88.62 99.05 96.17 0.20 0.15 0.07 0.34 0.14 0.10
ZNF717 ENST00000422325 93.41 95.55 96.16 0.13 0.23 0.07 0.15 0.21 0.10
GOLGA8S ENST00000562295 89.50 97.36 96.16 0.16 0.22 0.07 0.30 0.19 0.10
NUTM2E ENST00000429984 90.48 96.04 96.15 0.16 0.21 0.07 0.25 0.20 0.10
IL3RA ENST00000331035 95.58 91.28 96.15 0.11 0.23 0.07 0.11 0.34 0.10
NAT8 ENST00000272425 88.12 98.48 96.14 0.20 0.21 0.07 0.35 0.15 0.10
LCE3B ENST00000335633 90.01 95.08 96.14 0.16 0.23 0.07 0.26 0.21 0.10
RBMY1J ENST00000250831 92.69 93.73 96.13 0.15 0.28 0.07 0.17 0.26 0.10
RP11-15E18.4 ENST00000592917 90.98 95.33 96.13 0.16 0.24 0.07 0.21 0.21 0.10
C9orf16 ENST00000372994 91.20 95.09 96.12 0.15 0.23 0.07 0.21 0.21 0.10
NUPR1L ENST00000329309 91.62 96.33 96.12 0.15 0.22 0.07 0.20 0.19 0.10
RP11-268J15.5 ENST00000373137 86.88 99.80 96.11 0.24 0.17 0.07 0.40 0.11 0.10
ZNF587B ENST00000442832 97.46 89.26 96.11 0.10 0.27 0.07 0.11 0.36 0.10
TRIM49D1 ENST00000530311 92.78 93.62 96.10 0.15 0.28 0.07 0.17 0.28 0.11

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