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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
GRM1 ENST00000361719 11.63 19.22 13.01 1.68 1.47 2.09 0.59 0.76 0.52
SNRNP70 ENST00000598441 11.63 5.84 5.98 1.68 2.86 3.26 0.59 0.35 0.30
PPIH ENST00000304979 11.64 64.38 36.12 1.70 0.49 0.89 0.59 1.22 1.79
KCNG3 ENST00000306078 11.64 26.48 16.91 1.70 1.18 1.68 0.59 1.10 0.71
OLA1 ENST00000284719 11.65 29.25 18.38 1.70 1.14 1.66 0.58 1.36 0.81
ASCL1 ENST00000266744 11.65 29.79 18.73 1.70 1.13 1.57 0.58 1.40 0.81
PWWP2A ENST00000307063 11.66 11.72 9.05 1.70 2.07 2.40 0.59 0.57 0.38
SNRPA1 ENST00000254193 11.66 6.79 6.61 1.70 2.66 3.00 0.59 0.37 0.32
RPS6KA1 ENST00000531382 11.67 25.81 16.58 1.71 1.21 1.72 0.59 1.05 0.70
GTF2A2 ENST00000396060 11.67 72.85 40.50 1.70 0.49 0.80 0.59 1.05 2.04
PLCB4 ENST00000378501 11.68 21.87 14.49 1.68 1.46 2.00 0.59 0.81 0.59
CLASP1 ENST00000263710 11.68 2.93 4.65 1.68 3.50 3.69 0.59 0.29 0.25
PKNOX2 ENST00000298282 11.69 10.40 8.42 1.68 2.24 2.54 0.59 0.50 0.38
ABI1 ENST00000376142 11.69 17.43 12.13 1.68 1.59 2.28 0.59 0.74 0.48
SOX6 ENST00000396356 11.70 6.24 6.22 1.68 2.73 3.15 0.59 0.36 0.32
PTBP3 ENST00000458258 11.70 17.36 12.11 1.68 1.59 2.28 0.59 0.75 0.48
SLC16A2 ENST00000587091 11.71 8.11 7.26 1.68 2.52 2.78 0.59 0.44 0.33
PPP5C ENST00000012443 11.71 6.30 6.32 1.67 2.69 3.11 0.59 0.36 0.32
HSPE1 ENST00000233893 11.72 27.78 17.64 1.67 1.24 1.66 0.59 1.18 0.77
HHEX ENST00000282728 11.72 29.59 18.69 1.67 1.10 1.57 0.59 1.39 0.81
MEF2D ENST00000348159 11.73 9.82 8.15 1.67 2.40 2.59 0.59 0.49 0.37
SAMD13 ENST00000370673 11.73 67.31 37.75 1.67 0.56 0.84 0.59 1.21 2.01
FBXO3 ENST00000265651 11.74 12.12 9.39 1.67 2.07 2.29 0.59 0.57 0.39
OPHN1 ENST00000355520 11.75 3.42 4.84 1.66 3.41 3.68 0.59 0.29 0.24
ARRDC3 ENST00000265138 11.75 11.48 8.99 1.66 2.11 2.44 0.59 0.57 0.38

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