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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
DLC1 ENST00000276297 56.05 8.41 30.45 0.58 2.52 0.80 1.62 0.46 1.46
DGCR2 ENST00000263196 56.05 50.03 52.30 0.58 0.66 0.59 1.62 2.01 1.91
RBP2 ENST00000232217 56.06 47.43 50.81 0.58 0.66 0.67 1.62 2.02 1.85
CR2 ENST00000367057 56.06 46.47 50.30 0.58 0.73 0.65 1.62 2.02 1.92
OR10V1 ENST00000307552 56.07 83.79 72.58 0.58 0.27 0.46 1.62 0.47 0.82
SFTPB ENST00000393822 56.07 38.67 46.08 0.58 0.70 0.68 1.62 1.66 1.97
IL12A ENST00000305579 56.08 43.34 48.61 0.58 0.59 0.67 1.61 1.94 1.85
ATMIN ENST00000299575 56.08 41.52 47.59 0.58 0.62 0.65 1.61 1.83 1.88
PRIM2 ENST00000607273 56.09 47.70 50.95 0.58 0.61 0.66 1.61 1.97 1.85
NDUFV1 ENST00000322776 56.09 69.03 63.83 0.58 0.54 0.49 1.61 1.14 1.38
F2R ENST00000319211 56.10 57.88 56.86 0.58 0.57 0.51 1.61 1.48 1.70
TPBG ENST00000369750 56.10 63.34 60.15 0.58 0.48 0.48 1.61 1.30 1.61
PCDH15 ENST00000361849 56.11 43.28 48.62 0.58 0.61 0.67 1.61 1.94 1.85
MRPS30 ENST00000507110 56.11 60.57 58.39 0.58 0.52 0.52 1.61 1.41 1.65
DDX54 ENST00000314045 56.12 35.53 44.29 0.58 0.77 0.61 1.61 1.57 2.04
PRADC1 ENST00000258083 56.12 80.57 70.69 0.58 0.37 0.43 1.61 0.57 0.88
SLC2A3 ENST00000075120 56.13 29.18 40.82 0.58 1.13 0.80 1.61 1.34 2.04
KRT6A ENST00000330722 56.13 43.87 48.90 0.58 0.61 0.71 1.61 1.96 1.84
SYTL5 ENST00000456733 56.14 34.08 43.49 0.58 0.84 0.62 1.61 1.54 2.00
ARL15 ENST00000504924 56.14 66.48 62.09 0.58 0.57 0.48 1.61 1.21 1.44
CDKL4 ENST00000378803 56.15 86.06 73.89 0.58 0.27 0.42 1.61 0.44 0.70
UFSP2 ENST00000264689 56.15 45.07 49.53 0.58 0.67 0.67 1.62 1.97 1.85
C16orf45 ENST00000300006 56.16 43.11 48.53 0.58 0.61 0.68 1.62 1.90 1.86
GALR1 ENST00000299727 56.16 65.98 61.81 0.58 0.56 0.47 1.62 1.22 1.46
ARHGAP27 ENST00000376922 56.17 29.34 40.97 0.58 1.11 0.76 1.62 1.36 2.05

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