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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
C1orf234 ENST00000566855 94.25 90.32 95.04 0.10 0.25 0.09 0.12 0.38 0.10
TMEM88B ENST00000378821 94.25 84.58 92.07 0.10 0.28 0.14 0.12 0.42 0.16
CTC-534A2.2 ENST00000510585 94.26 54.99 77.82 0.10 0.57 0.38 0.12 1.64 0.54
AF165138.7 ENST00000400562 94.26 88.69 94.20 0.10 0.25 0.09 0.12 0.35 0.12
CTD-3203P2.2 ENST00000566854 94.27 92.44 96.09 0.10 0.27 0.07 0.12 0.30 0.11
ZNF14 ENST00000344099 94.27 70.75 85.82 0.10 0.48 0.33 0.12 1.08 0.33
C17orf82 ENST00000335108 94.28 99.11 98.81 0.10 0.15 0.10 0.12 0.14 0.05
FAM71E2 ENST00000424985 94.28 51.58 75.96 0.10 0.62 0.38 0.12 1.87 0.62
ANKRD18B ENST00000290943 94.29 45.01 72.34 0.10 0.68 0.44 0.12 1.97 0.82
CST1 ENST00000304749 94.29 97.11 98.10 0.10 0.24 0.09 0.12 0.18 0.05
FUT5 ENST00000252675 94.30 97.54 98.26 0.10 0.22 0.09 0.11 0.19 0.05
ACRC ENST00000373695 94.30 4.43 48.24 0.10 3.27 0.67 0.11 0.32 1.87
CD8B ENST00000331469 94.31 79.92 90.17 0.10 0.37 0.18 0.11 0.61 0.21
CST2 ENST00000304725 94.31 96.48 97.91 0.10 0.22 0.09 0.11 0.19 0.04
GOLGA8M ENST00000563027 94.32 80.41 90.41 0.10 0.37 0.15 0.11 0.59 0.21
PTTG2 ENST00000504686 94.32 99.36 98.91 0.10 0.16 0.10 0.11 0.12 0.04
PSORS1C1 ENST00000259881 94.33 91.93 95.86 0.10 0.23 0.07 0.11 0.33 0.11
NPIPB11 ENST00000524087 94.33 58.67 79.83 0.10 0.54 0.38 0.11 1.43 0.52
FAM183B ENST00000409072 94.34 99.63 98.29 0.10 0.16 0.09 0.11 0.12 0.05
PRAMEF14 ENST00000334600 94.34 93.57 96.78 0.10 0.28 0.08 0.11 0.28 0.08
TAS2R9 ENST00000240691 94.35 97.52 98.27 0.10 0.22 0.09 0.11 0.19 0.05
CGB2 ENST00000359342 94.35 92.24 96.02 0.10 0.25 0.07 0.11 0.31 0.11
NCBP2L ENST00000509000 94.36 98.80 98.94 0.10 0.16 0.10 0.11 0.14 0.04
NBPF15 ENST00000442702 94.36 96.15 97.81 0.10 0.21 0.09 0.11 0.20 0.04
SP140L ENST00000415673 94.37 42.38 70.70 0.10 0.59 0.43 0.11 1.90 0.87

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