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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
SLC17A7 ENST00000221485 2.09 1.64 0.52 4.22 3.85 4.70 0.25 0.26 0.17
TRIM24 ENST00000343526 2.17 1.58 0.53 4.16 3.87 4.70 0.27 0.26 0.17
STAG1 ENST00000383202 1.95 1.79 0.53 4.28 3.80 4.69 0.24 0.26 0.17
MATR3 ENST00000394805 3.22 0.53 0.54 3.87 4.14 4.71 0.30 0.27 0.17
CTCF ENST00000264010 0.86 2.92 0.54 4.34 3.50 4.71 0.18 0.29 0.17
RBM10 ENST00000377604 2.08 1.76 0.55 4.22 3.82 4.72 0.24 0.26 0.17
POLR2A ENST00000322644 0.33 3.52 0.55 4.42 3.39 4.72 0.17 0.29 0.17
INO80 ENST00000361937 3.77 0.10 0.56 3.78 4.12 4.71 0.30 0.28 0.17
WBP11 ENST00000261167 0.85 3.06 0.56 4.35 3.46 4.71 0.18 0.28 0.17
TM9SF2 ENST00000376387 3.39 0.55 0.57 3.83 4.15 4.71 0.30 0.27 0.17
SUPT16H ENST00000216297 2.19 1.75 0.57 4.17 3.83 4.70 0.28 0.26 0.17
MED12 ENST00000374080 3.80 0.17 0.58 3.77 4.11 4.70 0.30 0.28 0.17
ZNF148 ENST00000360647 2.79 1.18 0.58 3.98 4.02 4.69 0.28 0.28 0.17
UBXN7 ENST00000296328 2.27 1.74 0.59 4.14 3.83 4.69 0.28 0.26 0.17
MLLT3 ENST00000380338 1.89 2.12 0.59 4.28 3.68 4.68 0.24 0.28 0.18
NCKAP1 ENST00000360982 3.96 0.07 0.60 3.79 4.12 4.68 0.30 0.27 0.18
RBM22 ENST00000199814 1.30 2.73 0.60 4.38 3.54 4.68 0.17 0.29 0.18
PHIP ENST00000275034 2.84 1.19 0.61 3.96 4.03 4.67 0.28 0.28 0.19
EED ENST00000263360 2.37 1.68 0.61 4.09 3.83 4.67 0.27 0.25 0.19
ADAM10 ENST00000260408 2.49 1.59 0.62 4.09 3.86 4.66 0.27 0.26 0.19
LRRC7 ENST00000035383 1.64 2.52 0.62 4.29 3.57 4.66 0.22 0.29 0.19
KIF2A ENST00000407818 0.55 3.65 0.63 4.38 3.35 4.65 0.19 0.31 0.19
CLCN4 ENST00000380833 1.34 2.87 0.64 4.35 3.51 4.65 0.18 0.28 0.19
CACNA1C ENST00000347598 2.98 1.23 0.64 3.90 4.00 4.65 0.30 0.27 0.19
AGO2 ENST00000220592 2.69 1.55 0.65 4.02 3.88 4.64 0.29 0.26 0.19

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