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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
PLEKHA6 ENST00000272203 46.62 18.77 30.91 0.56 1.53 0.80 1.82 0.74 1.51
CORO1B ENST00000393893 46.62 41.47 42.31 0.56 0.62 0.70 1.82 1.82 2.01
TSSK3 ENST00000373534 46.63 58.94 51.98 0.56 0.52 0.62 1.81 1.42 1.92
PRDX2 ENST00000301522 46.63 49.55 46.82 0.56 0.66 0.67 1.81 2.02 1.88
CCDC117 ENST00000249064 46.64 24.91 33.95 0.56 1.32 0.90 1.81 1.07 1.73
TMC2 ENST00000358864 46.65 61.99 53.74 0.56 0.56 0.62 1.81 1.36 1.80
SSFA2 ENST00000431877 46.65 28.60 35.74 0.57 1.16 0.85 1.81 1.29 1.78
ZNF174 ENST00000268655 46.66 35.61 39.47 0.57 0.78 0.80 1.81 1.58 2.03
SPATA5 ENST00000274008 46.66 60.04 52.69 0.57 0.53 0.59 1.82 1.37 1.89
SMPD1 ENST00000342245 46.67 63.58 54.73 0.57 0.51 0.56 1.82 1.25 1.73
RASEF ENST00000376447 46.67 39.34 41.22 0.57 0.70 0.76 1.82 1.65 2.01
MYO3A ENST00000265944 46.68 56.47 50.61 0.57 0.52 0.66 1.82 1.54 1.85
UNC80 ENST00000439458 46.68 12.53 27.77 0.57 2.09 0.90 1.82 0.58 1.27
BYSL ENST00000230340 46.69 43.14 43.28 0.56 0.62 0.65 1.82 1.89 2.01
ASPH ENST00000379454 46.69 45.00 44.31 0.57 0.68 0.61 1.82 1.97 2.04
UBTD1 ENST00000370664 46.70 26.87 34.97 0.57 1.23 0.90 1.82 1.12 1.74
POLR3D ENST00000397802 46.70 68.71 57.68 0.57 0.53 0.49 1.82 1.17 1.67
TOX2 ENST00000341197 46.71 32.00 37.62 0.57 0.92 0.82 1.82 1.48 2.01
CPB2 ENST00000181383 46.71 73.13 60.39 0.57 0.53 0.44 1.82 1.02 1.58
RNF149 ENST00000295317 46.72 45.11 44.41 0.57 0.68 0.61 1.82 1.97 2.04
GDPGP1 ENST00000558017 46.72 90.31 70.87 0.57 0.25 0.43 1.82 0.38 0.86
MASP1 ENST00000296280 46.73 52.70 48.62 0.57 0.67 0.67 1.82 1.80 1.85
FAM89A ENST00000366654 46.73 72.65 60.09 0.57 0.47 0.48 1.82 1.04 1.61
TOMM6 ENST00000398884 46.74 82.02 66.02 0.56 0.35 0.51 1.82 0.50 1.22
NECAP2 ENST00000443980 46.74 76.41 62.42 0.56 0.43 0.48 1.82 0.86 1.40

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