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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
PUF60 ENST00000526683 0.13 8.52 2.06 4.54 2.52 4.11 0.16 0.46 0.23
PRPS1 ENST00000372435 0.14 16.63 5.66 4.53 1.72 3.37 0.16 0.71 0.27
UBE2I ENST00000355803 0.14 10.75 2.86 4.53 2.13 4.01 0.16 0.51 0.23
RBM39 ENST00000253363 0.15 6.05 1.22 4.52 2.81 4.42 0.16 0.35 0.21
ARIH1 ENST00000379887 0.15 2.01 0.19 4.54 3.72 4.88 0.16 0.28 0.18
YY1 ENST00000262238 0.16 5.49 1.05 4.54 3.04 4.44 0.16 0.33 0.21
MEIS1 ENST00000272369 0.17 2.93 0.39 4.53 3.49 4.77 0.16 0.29 0.18
UBE2D2 ENST00000398733 0.17 10.85 2.92 4.53 2.13 4.00 0.16 0.50 0.23
ARF1 ENST00000541182 0.18 20.54 7.71 4.52 1.43 2.68 0.16 0.78 0.33
GNAO1 ENST00000262494 0.18 9.71 2.54 4.52 2.45 4.01 0.16 0.50 0.23
SRSF3 ENST00000373715 0.19 12.57 3.72 4.52 2.10 3.80 0.16 0.58 0.23
SMNDC1 ENST00000369603 0.19 26.68 11.08 4.51 1.18 2.20 0.16 1.12 0.45
CREB1 ENST00000432329 0.20 7.58 1.77 4.51 2.51 4.22 0.16 0.42 0.23
SCN8A ENST00000354534 0.20 1.58 0.12 4.50 3.87 4.87 0.16 0.26 0.18
U2AF2 ENST00000308924 0.21 2.47 0.27 4.50 3.57 4.85 0.16 0.29 0.18
UBE2K ENST00000261427 0.21 8.51 2.10 4.49 2.52 4.10 0.16 0.46 0.23
RBX1 ENST00000216225 0.22 14.32 4.59 4.49 2.05 3.70 0.16 0.61 0.25
UBE2G1 ENST00000396981 0.22 11.81 3.46 4.48 2.09 3.85 0.16 0.57 0.23
OGT ENST00000373719 0.23 0.58 0.03 4.48 4.15 4.89 0.16 0.28 0.15
NRF1 ENST00000393232 0.23 4.93 0.91 4.50 3.26 4.47 0.16 0.31 0.21
ACTC1 ENST00000290378 0.24 22.62 8.78 4.50 1.47 2.49 0.16 0.86 0.37
YWHAZ ENST00000395957 0.24 15.38 5.07 4.49 1.90 3.64 0.17 0.68 0.25
DLX6 ENST00000518156 0.25 17.68 6.24 4.49 1.56 3.15 0.17 0.73 0.32
DDX39B ENST00000396172 0.25 6.78 1.51 4.48 2.67 4.34 0.17 0.37 0.22
RAB14 ENST00000373840 0.26 6.46 1.39 4.48 2.62 4.36 0.17 0.37 0.23

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