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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
VCX ENST00000381059 89.49 90.80 92.90 0.16 0.25 0.14 0.30 0.35 0.15
TPSG1 ENST00000234798 89.49 97.12 96.06 0.16 0.24 0.07 0.30 0.18 0.11
GOLGA8S ENST00000562295 89.50 97.36 96.16 0.16 0.22 0.07 0.30 0.19 0.10
PRAMEF19 ENST00000540591 89.50 96.28 95.67 0.16 0.22 0.07 0.30 0.19 0.11
ZNF732 ENST00000419098 89.51 69.95 83.10 0.16 0.53 0.30 0.30 1.14 0.40
BX088651.1 ENST00000540551 89.52 98.61 96.96 0.16 0.20 0.08 0.30 0.15 0.07
FAM86B1 ENST00000448228 89.52 93.26 94.14 0.16 0.28 0.09 0.30 0.30 0.12
ZNF586 ENST00000396154 89.53 90.00 92.46 0.16 0.25 0.14 0.30 0.37 0.15
GOLGA8T ENST00000569052 89.53 94.38 94.67 0.16 0.23 0.09 0.30 0.24 0.11
NPIPB6 ENST00000532254 89.54 95.59 95.28 0.16 0.23 0.08 0.30 0.21 0.10
SOHLH1 ENST00000425225 89.54 42.22 67.71 0.16 0.61 0.52 0.30 1.89 1.12
C9orf50 ENST00000372478 89.55 75.95 85.99 0.16 0.44 0.33 0.30 0.86 0.33
IFI44 ENST00000370747 89.55 79.22 87.50 0.16 0.39 0.28 0.30 0.69 0.30
VENTX ENST00000325980 89.56 92.35 93.72 0.16 0.25 0.10 0.30 0.30 0.14
ZNF727 ENST00000550760 89.56 89.43 92.16 0.16 0.27 0.14 0.30 0.37 0.16
ZNF764 ENST00000252797 89.57 65.91 81.09 0.16 0.54 0.39 0.30 1.23 0.49
KRTAP4-3 ENST00000391356 89.57 99.63 96.64 0.16 0.16 0.08 0.30 0.12 0.08
C15orf56 ENST00000319503 89.58 91.46 93.23 0.16 0.23 0.14 0.30 0.32 0.15
PRTN3 ENST00000234347 89.58 85.12 90.39 0.16 0.25 0.15 0.30 0.45 0.21
CKLF-CMTM1 ENST00000527729 89.59 89.40 92.17 0.16 0.27 0.14 0.30 0.37 0.16
NBPF20 ENST00000369202 89.59 97.39 96.21 0.16 0.22 0.07 0.30 0.19 0.10
ZNF788 ENST00000339302 89.60 97.82 96.54 0.16 0.21 0.07 0.30 0.18 0.07
OR2T5 ENST00000366473 89.60 80.09 88.00 0.16 0.37 0.24 0.30 0.60 0.31
LEMD1 ENST00000367153 89.61 82.57 89.19 0.16 0.34 0.19 0.30 0.51 0.25
SLC51B ENST00000334287 89.61 73.20 84.76 0.16 0.54 0.34 0.30 1.02 0.40

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