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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
PCDH9 ENST00000544246 14.34 17.12 13.35 1.57 1.61 2.05 0.73 0.75 0.55
RGS10 ENST00000369103 14.34 26.89 18.58 1.56 1.23 1.58 0.73 1.12 0.81
ACVR2B ENST00000352511 14.35 17.65 13.67 1.56 1.58 2.02 0.73 0.73 0.58
MAPKAPK5 ENST00000551404 14.35 19.13 14.48 1.56 1.49 2.00 0.73 0.76 0.59
CLCN5 ENST00000376088 14.36 7.95 8.51 1.56 2.54 2.51 0.73 0.44 0.37
PIP4K2A ENST00000376573 14.36 28.71 19.55 1.56 1.15 1.53 0.73 1.29 0.84
SCARF2 ENST00000266214 14.37 5.56 7.33 1.56 2.99 2.81 0.73 0.33 0.34
RFC5 ENST00000454402 14.37 38.93 24.71 1.56 0.70 1.05 0.73 1.65 1.10
JOSD1 ENST00000216039 14.38 42.68 26.69 1.57 0.61 1.00 0.73 1.91 1.27
SLC12A2 ENST00000262461 14.38 13.41 11.57 1.57 2.05 2.21 0.73 0.60 0.45
FLRT3 ENST00000378053 14.39 26.97 18.68 1.57 1.23 1.57 0.73 1.10 0.81
ZNF800 ENST00000393313 14.39 3.49 6.22 1.57 3.38 3.15 0.73 0.29 0.32
COLEC12 ENST00000400256 14.40 15.64 12.56 1.57 1.87 2.21 0.73 0.68 0.52
C16orf80 ENST00000262498 14.41 54.58 32.69 1.56 0.59 0.86 0.73 1.66 1.63
RPS16 ENST00000251453 14.41 29.75 20.14 1.56 1.13 1.49 0.73 1.40 0.86
USP5 ENST00000229268 14.42 13.98 11.81 1.56 2.06 2.21 0.73 0.60 0.46
P4HA1 ENST00000412021 14.42 14.87 12.21 1.56 1.92 2.26 0.73 0.62 0.50
CENPA ENST00000335756 14.43 68.82 39.96 1.56 0.53 0.81 0.73 1.19 2.00
EDC3 ENST00000315127 14.43 34.04 22.42 1.56 0.82 1.15 0.73 1.55 0.97
PLCG1 ENST00000373272 14.44 19.11 14.50 1.56 1.51 2.00 0.73 0.76 0.59
PIAS2 ENST00000585916 14.44 9.13 9.22 1.56 2.48 2.32 0.73 0.47 0.38
ADAM17 ENST00000310823 14.45 9.01 9.17 1.56 2.44 2.33 0.73 0.47 0.38
GAS7 ENST00000432992 14.45 16.60 13.11 1.56 1.76 2.10 0.73 0.71 0.52
VAPB ENST00000475243 14.46 28.06 19.23 1.57 1.19 1.54 0.73 1.20 0.85
TMEM183A ENST00000367242 14.46 17.82 13.82 1.57 1.52 2.09 0.73 0.72 0.57

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