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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
GPR112 ENST00000394143 72.44 63.45 70.19 0.32 0.49 0.43 0.79 1.27 0.91
FGFRL1 ENST00000398484 72.45 38.19 54.87 0.32 0.77 0.51 0.79 1.71 1.74
TNFRSF12A ENST00000326577 72.45 74.66 76.65 0.32 0.54 0.37 0.79 0.97 0.61
RPL28 ENST00000558815 72.46 31.13 50.85 0.32 1.01 0.67 0.79 1.36 1.85
CROCC ENST00000375541 72.47 30.50 50.49 0.32 1.09 0.67 0.79 1.37 1.86
NSUN6 ENST00000377304 72.47 79.51 79.28 0.32 0.38 0.38 0.79 0.66 0.54
MRPL30 ENST00000410042 72.48 72.94 75.71 0.32 0.51 0.38 0.79 1.02 0.64
C8orf58 ENST00000289989 72.48 58.19 67.08 0.32 0.54 0.51 0.79 1.45 1.16
GPR25 ENST00000304244 72.49 68.60 73.32 0.32 0.53 0.43 0.80 1.18 0.78
CCDC173 ENST00000447353 72.49 63.33 70.14 0.32 0.48 0.46 0.80 1.31 0.90
UBXN11 ENST00000374222 72.50 61.30 68.95 0.32 0.54 0.46 0.80 1.39 1.04
GTSF1L ENST00000373003 72.50 89.29 84.16 0.32 0.27 0.34 0.80 0.37 0.42
C15orf26 ENST00000286732 72.51 43.81 58.24 0.32 0.61 0.47 0.80 1.96 1.64
MIS18BP1 ENST00000310806 72.51 41.00 56.57 0.32 0.61 0.52 0.80 1.80 1.70
C2orf78 ENST00000409561 72.52 48.59 61.20 0.32 0.65 0.43 0.80 2.01 1.49
APOA4 ENST00000357780 72.52 66.89 72.39 0.32 0.53 0.44 0.80 1.24 0.83
ZXDA ENST00000358697 72.53 62.15 69.54 0.32 0.53 0.44 0.80 1.35 0.96
ARVCF ENST00000263207 72.53 42.30 57.32 0.32 0.61 0.51 0.80 1.89 1.68
MTG1 ENST00000317502 72.54 33.99 52.57 0.32 0.84 0.61 0.80 1.55 1.90
ERP27 ENST00000266397 72.54 91.01 85.11 0.32 0.25 0.33 0.80 0.35 0.38
ZNF782 ENST00000481138 72.55 59.18 67.70 0.32 0.49 0.52 0.80 1.44 1.12
CDK11A ENST00000404249 72.55 72.58 75.50 0.32 0.47 0.38 0.80 1.04 0.66
DDRGK1 ENST00000354488 72.56 56.74 66.35 0.32 0.53 0.53 0.80 1.55 1.20
TEX15 ENST00000256246 72.56 40.09 56.00 0.32 0.63 0.49 0.80 1.71 1.77
ENPEP ENST00000265162 72.57 64.96 71.22 0.32 0.49 0.44 0.80 1.24 0.86

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