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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
AC003102.1 ENST00000399246 90.13 97.78 96.90 0.16 0.21 0.08 0.25 0.17 0.07
AC104472.1 ENST00000399242 90.14 97.79 96.90 0.16 0.21 0.08 0.25 0.17 0.07
AC005481.5 ENST00000409610 90.15 83.58 90.05 0.16 0.27 0.18 0.25 0.47 0.22
RGPD6 ENST00000329516 90.15 87.39 91.69 0.16 0.23 0.14 0.25 0.41 0.18
AC022400.2 ENST00000595757 90.16 93.32 94.50 0.16 0.28 0.10 0.25 0.29 0.12
THEGL ENST00000512175 90.16 68.10 82.64 0.16 0.52 0.32 0.25 1.20 0.43
LCE3C ENST00000333881 90.17 79.82 88.27 0.16 0.35 0.22 0.25 0.62 0.30
C7orf72 ENST00000297001 90.17 69.69 83.66 0.16 0.53 0.34 0.25 1.12 0.40
PP2D1 ENST00000389050 90.18 65.44 81.25 0.16 0.53 0.38 0.25 1.25 0.49
hsa-mir-150 ENST00000602157 90.18 96.49 96.00 0.16 0.22 0.07 0.25 0.19 0.11
SDHAF1 ENST00000378887 90.19 94.03 94.62 0.16 0.25 0.09 0.25 0.26 0.11
C19orf38 ENST00000397820 90.19 52.33 74.23 0.16 0.62 0.39 0.25 1.82 0.69
POTEB ENST00000439682 90.20 90.87 93.36 0.16 0.25 0.11 0.25 0.35 0.15
ZBED6 ENST00000550078 90.20 30.44 61.02 0.16 1.09 0.43 0.25 1.39 1.56
AL109927.1 ENST00000601459 90.21 97.79 96.93 0.16 0.21 0.08 0.25 0.18 0.07
PP13439 ENST00000331659 90.21 97.80 96.94 0.16 0.21 0.08 0.25 0.18 0.07
ATOH7 ENST00000373673 90.22 85.69 91.79 0.16 0.27 0.14 0.25 0.44 0.18
GSTT1 ENST00000248935 90.22 74.56 85.80 0.16 0.52 0.33 0.25 1.00 0.33
RP11-597K23.2 ENST00000559788 90.23 92.57 94.26 0.16 0.29 0.10 0.25 0.31 0.12
AL356356.1 ENST00000538795 90.23 57.51 78.00 0.16 0.56 0.38 0.26 1.48 0.54
SPATA31A7 ENST00000355045 90.24 96.43 97.82 0.16 0.22 0.09 0.26 0.19 0.04
RP11-362K2.2 ENST00000546977 90.24 87.77 91.89 0.16 0.24 0.14 0.26 0.37 0.17
AC022431.2 ENST00000438651 90.25 79.27 88.03 0.16 0.38 0.24 0.26 0.67 0.31
PNRC2 ENST00000334351 90.25 91.43 93.74 0.16 0.23 0.10 0.26 0.33 0.13
C1QTNF4 ENST00000302514 90.26 56.53 76.48 0.16 0.52 0.38 0.26 1.54 0.61

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