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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
PANK2 ENST00000316562 39.13 53.20 44.75 0.90 0.66 0.63 1.77 1.75 2.05
SPOCK3 ENST00000357154 39.14 26.55 31.06 0.90 1.19 0.84 1.77 1.12 1.51
PRRC1 ENST00000296666 39.14 77.41 58.33 0.90 0.42 0.49 1.77 0.76 1.64
SYNDIG1 ENST00000376862 39.15 38.95 37.34 0.90 0.70 0.84 1.77 1.64 2.01
LMO2 ENST00000257818 39.15 55.03 45.79 0.90 0.57 0.68 1.76 1.63 1.98
TGM1 ENST00000206765 39.16 49.20 42.43 0.90 0.66 0.68 1.76 2.03 2.01
TTC37 ENST00000358746 39.16 41.15 38.45 0.90 0.59 0.84 1.76 1.83 2.04
TKT ENST00000423516 39.17 29.13 32.34 0.90 1.14 0.90 1.76 1.34 1.61
STK10 ENST00000176763 39.17 41.52 38.62 0.90 0.62 0.84 1.76 1.83 2.01
CHST14 ENST00000306243 39.18 33.23 34.45 0.90 0.82 0.90 1.76 1.49 1.75
TBC1D12 ENST00000225235 39.18 31.39 33.43 0.90 0.96 0.89 1.76 1.41 1.71
CDON ENST00000392693 39.19 41.98 38.90 0.90 0.61 0.80 1.77 1.83 2.06
KIF13A ENST00000259711 39.19 5.78 20.61 0.90 2.86 1.48 1.77 0.34 0.88
PRRG1 ENST00000542554 39.20 62.84 50.01 0.90 0.51 0.61 1.77 1.29 1.91
MYH1 ENST00000226207 39.20 60.43 48.69 0.90 0.53 0.68 1.77 1.41 1.85
OSCP1 ENST00000235532 39.21 62.39 49.73 0.90 0.53 0.66 1.77 1.32 1.85
LIMA1 ENST00000394943 39.21 41.84 38.79 0.90 0.61 0.82 1.77 1.80 2.03
NPC1 ENST00000269228 39.22 23.31 29.43 0.90 1.43 0.85 1.77 0.93 1.36
B4GALT4 ENST00000483209 39.22 63.18 50.20 0.90 0.47 0.63 1.77 1.30 1.90
ZCCHC8 ENST00000336229 39.23 5.98 20.73 0.90 2.81 1.46 1.76 0.35 0.88
PCBD2 ENST00000512783 39.23 73.81 56.28 0.90 0.53 0.49 1.76 1.02 1.75
TRMT6 ENST00000203001 39.24 39.25 37.51 0.90 0.68 0.84 1.75 1.64 2.01
SLC7A11 ENST00000280612 39.24 40.49 38.14 0.90 0.62 0.86 1.75 1.77 2.04
PLXDC2 ENST00000377252 39.25 22.20 28.87 0.90 1.53 0.82 1.75 0.81 1.31
DNAJB6 ENST00000262177 39.25 18.67 27.11 0.90 1.51 0.99 1.75 0.75 1.26

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