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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
GRIK1-AS2 ENST00000333765 87.55 98.42 95.83 0.23 0.21 0.07 0.37 0.14 0.11
ZAN ENST00000546292 87.56 57.69 75.60 0.23 0.56 0.38 0.37 1.48 0.64
OR5P3 ENST00000328375 87.56 69.76 82.03 0.23 0.53 0.35 0.37 1.13 0.46
IGSF5 ENST00000380588 87.57 86.57 90.12 0.23 0.24 0.18 0.37 0.41 0.21
C1orf174 ENST00000361605 87.57 80.96 87.42 0.23 0.35 0.28 0.37 0.57 0.31
PCDHB11 ENST00000354757 87.58 84.27 89.05 0.23 0.28 0.19 0.37 0.44 0.26
CTAGE1 ENST00000391403 87.58 97.85 95.54 0.23 0.21 0.08 0.37 0.17 0.11
CMA1 ENST00000250378 87.59 92.09 92.58 0.23 0.24 0.14 0.37 0.32 0.15
FABP6 ENST00000393980 87.59 83.00 88.42 0.23 0.32 0.22 0.37 0.49 0.30
CLEC4A ENST00000229332 87.60 70.56 82.49 0.23 0.52 0.33 0.37 1.09 0.43
PRSS57 ENST00000329267 87.60 87.94 90.85 0.23 0.25 0.15 0.37 0.37 0.20
KRTAP15-1 ENST00000334067 87.61 99.99 96.20 0.23 0.18 0.07 0.37 0.09 0.10
H3F3C ENST00000340398 87.61 97.67 95.43 0.23 0.21 0.08 0.37 0.19 0.11
ZFP41 ENST00000330701 87.62 89.52 91.46 0.23 0.27 0.15 0.37 0.36 0.18
ZFP41 ENST00000522452 87.62 89.55 91.47 0.23 0.27 0.15 0.37 0.36 0.18
RGPD8 ENST00000302558 87.63 58.42 76.03 0.23 0.54 0.38 0.37 1.38 0.62
RGPD1 ENST00000559485 87.63 77.45 85.84 0.23 0.42 0.33 0.37 0.76 0.33
SYCE1L ENST00000378644 87.64 87.06 90.39 0.23 0.22 0.15 0.37 0.40 0.21
ASPDH ENST00000389208 87.65 73.18 83.80 0.23 0.54 0.34 0.37 1.02 0.42
OTOG ENST00000399391 87.65 37.91 64.06 0.23 0.80 0.52 0.37 1.70 1.37
ZNF785 ENST00000395216 87.66 96.20 94.66 0.23 0.22 0.09 0.37 0.20 0.11
CARHSP1 ENST00000396593 87.66 93.14 93.16 0.23 0.28 0.14 0.37 0.30 0.15
PPP2R3B ENST00000390665 87.67 47.28 69.70 0.23 0.66 0.44 0.37 2.00 0.94
ZNF488 ENST00000395702 87.67 73.71 83.98 0.23 0.52 0.35 0.37 1.03 0.42
DHRS12 ENST00000444610 87.68 70.35 82.40 0.23 0.52 0.33 0.37 1.09 0.44

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