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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
ZNF548 ENST00000336128 86.65 58.48 75.51 0.24 0.54 0.38 0.41 1.39 0.66
ZNF223 ENST00000434772 86.65 91.07 91.68 0.24 0.25 0.14 0.40 0.36 0.18
DCAF4L2 ENST00000319675 86.66 99.61 95.90 0.24 0.16 0.07 0.41 0.12 0.10
SBK2 ENST00000413299 86.66 84.29 88.60 0.24 0.28 0.22 0.41 0.44 0.28
MIIP ENST00000235332 86.67 85.77 89.31 0.24 0.27 0.18 0.41 0.44 0.25
ZNF141 ENST00000240499 86.67 67.73 80.52 0.24 0.52 0.39 0.40 1.19 0.51
ZNF709 ENST00000428311 86.68 91.63 91.91 0.24 0.23 0.14 0.40 0.32 0.17
ZNF709 ENST00000397732 86.68 91.11 91.72 0.24 0.25 0.14 0.40 0.35 0.18
KPRP ENST00000368773 86.69 88.24 90.53 0.24 0.23 0.15 0.40 0.37 0.21
ZNF571 ENST00000328550 86.69 72.42 82.91 0.24 0.51 0.32 0.40 1.03 0.40
ANKRD24 ENST00000600132 86.70 46.21 68.44 0.24 0.73 0.47 0.40 2.04 1.06
NMRK2 ENST00000168977 86.71 94.88 93.53 0.24 0.23 0.13 0.40 0.23 0.15
FAM47E ENST00000424749 86.71 46.39 68.53 0.24 0.73 0.47 0.40 2.04 1.06
PNMAL2 ENST00000599531 86.72 97.91 95.50 0.24 0.20 0.08 0.40 0.17 0.11
CCL14 ENST00000536149 86.72 87.21 90.04 0.24 0.20 0.18 0.40 0.41 0.22
C20orf96 ENST00000360321 86.73 75.08 84.18 0.24 0.51 0.34 0.40 0.91 0.42
OR4C13 ENST00000555099 86.73 97.41 94.79 0.24 0.22 0.09 0.40 0.19 0.11
NXF3 ENST00000395065 86.74 31.03 59.03 0.24 1.04 0.48 0.40 1.36 1.65
ZNF620 ENST00000314529 86.74 60.07 76.50 0.24 0.52 0.38 0.40 1.38 0.61
GTF2IRD2B ENST00000312575 86.75 36.21 62.31 0.24 0.82 0.49 0.40 1.61 1.41
RP11-477N12.3 ENST00000399363 86.75 67.86 80.63 0.24 0.52 0.39 0.40 1.18 0.51
NPIPB8 ENST00000529716 86.76 94.76 93.50 0.24 0.23 0.11 0.40 0.24 0.15
EDDM3A ENST00000326842 86.76 99.44 95.88 0.24 0.16 0.07 0.40 0.12 0.11
OR8H1 ENST00000313022 86.77 96.32 94.32 0.24 0.22 0.10 0.40 0.19 0.12
LCE2C ENST00000368783 86.77 95.69 94.01 0.24 0.23 0.09 0.40 0.20 0.12

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