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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
APEX1 ENST00000216714 35.26 69.05 51.24 0.92 0.56 0.63 1.85 1.14 1.92
PGAP3 ENST00000300658 35.26 48.82 40.31 0.92 0.63 0.80 1.85 2.02 2.00
HSDL2 ENST00000398805 35.27 44.63 38.24 0.92 0.66 0.85 1.85 1.97 2.04
CDC14B ENST00000375241 35.27 15.19 23.32 0.92 1.90 1.19 1.85 0.67 0.98
TCP11L1 ENST00000334274 35.28 34.51 33.06 0.92 0.80 0.85 1.85 1.56 1.66
IL11RA ENST00000555003 35.28 81.24 58.31 0.92 0.34 0.49 1.85 0.54 1.64
ZC2HC1A ENST00000263849 35.29 17.00 24.15 0.92 1.63 1.11 1.85 0.73 1.05
FNDC5 ENST00000609187 35.29 43.70 37.73 0.92 0.62 0.84 1.85 1.96 2.01
FSHR ENST00000406846 35.30 62.27 47.57 0.92 0.53 0.65 1.85 1.34 1.89
TPX2 ENST00000300403 35.30 7.07 19.18 0.92 2.57 1.53 1.86 0.37 0.85
MYL1 ENST00000352451 35.31 67.25 50.32 0.92 0.56 0.66 1.86 1.22 1.92
SCN9A ENST00000409672 35.31 36.58 34.14 0.92 0.78 0.89 1.86 1.63 1.75
FBXO31 ENST00000311635 35.32 22.07 26.87 0.92 1.49 0.97 1.87 0.81 1.27
TAF10 ENST00000299424 35.32 21.95 26.79 0.92 1.47 0.96 1.87 0.81 1.28
LEPR ENST00000349533 35.33 11.18 21.37 0.92 2.09 1.34 1.87 0.54 0.91
TGIF1 ENST00000330513 35.33 49.75 40.70 0.92 0.66 0.81 1.87 2.03 2.05
SHROOM4 ENST00000376020 35.34 8.37 19.91 0.94 2.52 1.46 1.87 0.46 0.85
TMC1 ENST00000297784 35.34 51.31 41.54 0.94 0.63 0.75 1.87 1.90 2.01
GNPTAB ENST00000299314 35.35 43.89 37.85 0.94 0.61 0.85 1.87 1.96 2.01
RNF4 ENST00000511600 35.35 24.37 28.05 0.95 1.30 0.82 1.87 1.00 1.28
SLC35C2 ENST00000372227 35.36 48.78 40.36 0.95 0.63 0.80 1.87 2.01 2.02
RABL3 ENST00000273375 35.36 53.22 42.55 0.95 0.66 0.68 1.87 1.75 2.02
ZNF263 ENST00000219069 35.37 53.32 42.62 0.95 0.66 0.67 1.87 1.72 2.02
TLN2 ENST00000561311 35.38 10.59 21.13 0.96 2.15 1.42 1.87 0.51 0.90
UBE2Q2 ENST00000267938 35.38 52.92 42.39 0.96 0.65 0.68 1.87 1.79 2.02

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