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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
OR8G1 ENST00000341493 83.03 84.20 86.77 0.28 0.27 0.30 0.55 0.44 0.31
WISP2 ENST00000372868 83.04 76.45 83.12 0.29 0.43 0.30 0.55 0.85 0.40
ZNF500 ENST00000219478 83.04 55.78 72.02 0.29 0.52 0.43 0.55 1.58 0.81
PARM1 ENST00000307428 83.05 66.46 77.94 0.29 0.56 0.38 0.55 1.20 0.54
ACOT2 ENST00000238651 83.05 73.91 81.85 0.29 0.53 0.37 0.55 1.02 0.46
LCE3D ENST00000368787 83.06 93.96 91.42 0.29 0.25 0.15 0.55 0.26 0.18
IFIT3 ENST00000371818 83.06 66.49 77.96 0.29 0.57 0.38 0.55 1.22 0.54
AC004466.1 ENST00000599515 83.07 97.08 92.81 0.29 0.24 0.14 0.55 0.19 0.15
C2orf16 ENST00000408964 83.07 55.01 71.57 0.29 0.57 0.44 0.55 1.63 0.83
CCDC144A ENST00000443444 83.08 41.45 63.42 0.29 0.62 0.49 0.55 1.81 1.37
SLCO1B3 ENST00000381545 83.08 82.49 86.03 0.29 0.34 0.33 0.55 0.52 0.33
SUMO4 ENST00000326669 83.09 98.72 93.66 0.29 0.16 0.11 0.55 0.15 0.15
CCDC40 ENST00000397545 83.09 45.71 66.04 0.29 0.75 0.51 0.55 2.02 1.22
C8orf33 ENST00000331434 83.10 89.15 89.22 0.29 0.27 0.19 0.54 0.35 0.25
SIX5 ENST00000317578 83.11 44.15 65.07 0.29 0.61 0.51 0.54 1.96 1.31
MYOM2 ENST00000262113 83.11 79.62 84.73 0.29 0.37 0.34 0.54 0.66 0.40
THAP8 ENST00000292894 83.12 83.33 86.41 0.29 0.27 0.30 0.54 0.47 0.33
MYOD1 ENST00000250003 83.12 58.60 73.64 0.29 0.54 0.40 0.54 1.42 0.74
EDA2R ENST00000450752 83.13 74.47 82.18 0.29 0.53 0.35 0.54 0.99 0.45
CERS4 ENST00000251363 83.13 83.74 86.63 0.29 0.27 0.30 0.54 0.47 0.33
LRRC71 ENST00000337428 83.14 40.33 62.66 0.29 0.62 0.51 0.54 1.74 1.40
SELM ENST00000402395 83.14 93.50 91.26 0.29 0.28 0.15 0.54 0.28 0.18
PPM1N ENST00000451287 83.15 77.12 83.50 0.29 0.42 0.33 0.54 0.78 0.40
ITGB3BP ENST00000371092 83.15 79.16 84.50 0.29 0.39 0.33 0.54 0.69 0.40
TIRAP ENST00000392678 83.16 83.23 86.38 0.29 0.28 0.32 0.54 0.47 0.33

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