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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
SRM ENST00000376957 4.14 29.25 14.44 3.73 1.14 2.00 0.30 1.36 0.58
HCN1 ENST00000303230 4.14 4.72 2.15 3.72 3.27 4.07 0.30 0.31 0.23
SYNGAP1 ENST00000418600 4.15 0.16 0.66 3.72 4.12 4.63 0.30 0.28 0.20
BRD8 ENST00000254900 4.15 22.96 11.22 3.72 1.47 2.15 0.30 0.90 0.45
EPPK1 ENST00000525985 4.16 62.27 31.47 3.72 0.53 0.86 0.30 1.33 1.56
MARCH6 ENST00000274140 4.16 3.04 1.58 3.72 3.47 4.29 0.30 0.28 0.23
ATP6V1A ENST00000273398 4.17 15.99 7.45 3.71 1.86 2.78 0.30 0.68 0.34
ANKRD13C ENST00000370944 4.17 10.15 4.44 3.71 2.30 3.71 0.30 0.49 0.25
RPS9 ENST00000302907 4.18 20.78 10.05 3.71 1.44 2.26 0.30 0.81 0.42
DNM1L ENST00000549701 4.18 25.86 12.56 3.71 1.21 2.21 0.30 1.08 0.51
DAZAP1 ENST00000233078 4.19 1.77 1.15 3.71 3.82 4.42 0.30 0.26 0.21
PAFAH1B1 ENST00000397195 4.19 1.44 1.04 3.70 3.93 4.44 0.30 0.26 0.21
NCOR1 ENST00000268712 4.20 3.34 1.67 3.70 3.43 4.25 0.30 0.27 0.23
BRSK1 ENST00000309383 4.20 6.18 2.70 3.71 2.76 4.00 0.30 0.35 0.23
NEK7 ENST00000367385 4.21 17.59 8.25 3.71 1.57 2.57 0.30 0.73 0.37
MSL2 ENST00000309993 4.21 25.03 12.19 3.71 1.33 2.29 0.30 1.04 0.49
GRAMD1B ENST00000529750 4.22 6.54 2.81 3.71 2.62 4.03 0.30 0.37 0.23
SGMS1 ENST00000361781 4.22 15.63 7.27 3.70 1.87 2.80 0.30 0.68 0.34
KCNN2 ENST00000512097 4.23 10.24 4.54 3.72 2.29 3.70 0.30 0.49 0.25
ELK1 ENST00000247161 4.24 15.16 7.05 3.71 1.90 2.88 0.30 0.66 0.33
CSNK1E ENST00000396832 4.24 2.81 1.53 3.71 3.51 4.32 0.30 0.28 0.22
NAA15 ENST00000296543 4.25 11.43 5.08 3.71 2.10 3.64 0.30 0.56 0.25
G3BP1 ENST00000394123 4.25 27.42 13.47 3.71 1.25 2.05 0.30 1.17 0.57
NR3C1 ENST00000231509 4.26 13.22 5.99 3.72 2.06 3.25 0.30 0.60 0.30
CCND2 ENST00000261254 4.26 7.18 3.16 3.72 2.58 3.91 0.30 0.37 0.24

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