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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
NUFIP1 ENST00000379161 64.31 48.05 55.85 0.56 0.63 0.51 1.19 2.00 1.75
ZNF274 ENST00000326804 64.31 24.99 43.02 0.56 1.33 0.67 1.19 1.05 2.02
PTMS ENST00000309083 64.32 49.36 56.63 0.56 0.65 0.52 1.19 2.01 1.72
ELOVL2 ENST00000354666 64.33 74.14 71.80 0.56 0.53 0.44 1.19 1.03 0.82
DHX58 ENST00000251642 64.33 56.55 61.06 0.56 0.52 0.43 1.19 1.55 1.54
TSPYL1 ENST00000368608 64.34 70.84 69.79 0.56 0.49 0.44 1.19 1.07 0.93
PAK4 ENST00000593690 64.34 43.39 53.30 0.56 0.61 0.62 1.19 1.95 1.85
VNN3 ENST00000427187 64.35 60.14 63.40 0.56 0.52 0.49 1.19 1.39 1.37
CHI3L1 ENST00000255409 64.35 52.55 58.51 0.56 0.67 0.51 1.19 1.82 1.64
RRS1 ENST00000320270 64.36 38.14 50.28 0.56 0.77 0.65 1.19 1.72 1.92
STAC ENST00000273183 64.36 52.87 58.68 0.56 0.65 0.51 1.19 1.80 1.64
ITIH5 ENST00000256861 64.37 65.45 66.58 0.56 0.53 0.52 1.19 1.25 1.21
FAM72A ENST00000367128 64.37 90.58 80.77 0.56 0.25 0.39 1.19 0.37 0.52
TRIML1 ENST00000332517 64.38 75.77 72.80 0.56 0.43 0.43 1.19 0.88 0.81
FAM43B ENST00000332947 64.38 71.13 70.00 0.56 0.51 0.47 1.19 1.07 0.91
ADPRHL1 ENST00000375418 64.39 75.24 72.49 0.56 0.49 0.44 1.20 0.90 0.83
L3HYPDH ENST00000247194 64.39 75.71 72.74 0.56 0.44 0.43 1.20 0.88 0.81
DCT ENST00000446125 64.40 64.83 66.30 0.56 0.48 0.53 1.20 1.24 1.21
PAPOLB ENST00000404991 64.40 43.63 53.44 0.56 0.62 0.62 1.20 1.97 1.83
OR1L4 ENST00000259466 64.41 94.24 82.73 0.56 0.24 0.32 1.20 0.25 0.42
ADORA2B ENST00000304222 64.41 78.83 74.55 0.56 0.42 0.40 1.20 0.71 0.69
TBATA ENST00000299290 64.42 78.39 74.26 0.56 0.43 0.39 1.20 0.74 0.69
ADAMTSL4 ENST00000271643 64.42 60.65 63.78 0.56 0.53 0.49 1.20 1.41 1.38
SNX29 ENST00000566228 64.43 37.18 49.73 0.56 0.78 0.66 1.20 1.66 1.85
SNAP29 ENST00000215730 64.43 40.92 51.82 0.56 0.61 0.62 1.20 1.78 1.92

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