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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
RHEBL1 ENST00000301068 21.44 70.92 44.79 1.56 0.49 0.66 1.07 1.07 2.04
TMED9 ENST00000332598 21.45 44.69 31.29 1.56 0.66 0.86 1.07 1.97 1.55
SZRD1 ENST00000401088 21.45 34.51 26.16 1.57 0.80 0.99 1.07 1.56 1.27
ODF2 ENST00000434106 21.46 22.37 19.94 1.57 1.51 1.46 1.07 0.82 0.84
TSPAN33 ENST00000289407 21.46 50.20 34.03 1.57 0.67 0.90 1.07 1.99 1.72
PRRX1 ENST00000239461 21.47 33.26 25.44 1.57 0.84 1.02 1.07 1.50 1.18
LSM7 ENST00000252622 21.47 32.72 25.16 1.57 0.84 1.05 1.07 1.45 1.17
COG3 ENST00000349995 21.48 6.44 11.61 1.57 2.64 2.23 1.06 0.37 0.45
SCGN ENST00000377961 21.48 75.57 47.29 1.57 0.44 0.66 1.06 0.90 1.87
MYLIP ENST00000356840 21.49 28.42 23.07 1.57 1.16 1.20 1.06 1.24 0.99
KANSL2 ENST00000420613 21.49 20.74 19.11 1.57 1.46 1.53 1.06 0.81 0.85
KCTD16 ENST00000507359 21.50 5.46 11.13 1.57 3.04 2.19 1.06 0.33 0.45
DNMT3A ENST00000264709 21.50 74.03 46.42 1.57 0.53 0.67 1.06 1.03 1.92
ADRBK2 ENST00000324198 21.51 16.87 17.04 1.57 1.66 1.67 1.06 0.71 0.70
SPG21 ENST00000204566 21.51 39.94 28.85 1.57 0.63 0.82 1.06 1.69 1.31
ZNF3 ENST00000303915 21.52 58.03 38.05 1.57 0.53 0.85 1.06 1.45 2.02
STK4 ENST00000372806 21.52 26.81 22.33 1.57 1.23 1.16 1.06 1.12 0.97
DDX27 ENST00000371764 21.53 17.13 17.17 1.57 1.61 1.64 1.06 0.75 0.73
GMDS ENST00000380815 21.53 10.13 13.45 1.57 2.33 2.05 1.06 0.49 0.57
TM9SF1 ENST00000261789 21.54 50.41 34.18 1.57 0.65 0.89 1.06 1.95 1.75
SHANK2 ENST00000338508 21.54 22.51 20.09 1.57 1.51 1.49 1.06 0.84 0.85
FLT4 ENST00000261937 21.55 2.71 9.59 1.56 3.53 2.28 1.06 0.29 0.40
SRP68 ENST00000307877 21.55 19.62 18.55 1.56 1.43 1.61 1.06 0.74 0.81
MYNN ENST00000349841 21.56 20.48 18.99 1.56 1.43 1.54 1.06 0.78 0.84
GAPDH ENST00000229239 21.56 34.98 26.36 1.56 0.75 1.00 1.06 1.56 1.26

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