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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
GBF1 ENST00000369983 14.73 28.66 19.73 1.56 1.18 1.52 0.74 1.29 0.85
GPS2 ENST00000380728 14.73 27.40 19.06 1.56 1.25 1.54 0.74 1.17 0.85
VIM ENST00000544301 14.74 18.92 14.53 1.56 1.52 1.99 0.74 0.76 0.59
SFTA2 ENST00000359086 14.74 88.85 50.87 1.56 0.25 0.67 0.74 0.35 1.84
PHC2 ENST00000257118 14.75 16.24 13.08 1.56 1.80 2.10 0.74 0.69 0.52
KLF10 ENST00000285407 14.75 46.16 28.61 1.57 0.73 0.80 0.74 2.04 1.35
EIF2AK3 ENST00000303236 14.76 21.57 16.00 1.57 1.44 1.75 0.74 0.81 0.66
CLINT1 ENST00000523908 14.76 18.85 14.51 1.57 1.53 2.00 0.74 0.74 0.59
SOD1 ENST00000270142 14.77 63.62 37.43 1.57 0.51 0.86 0.74 1.24 2.01
DCTN1 ENST00000361874 14.77 16.21 13.07 1.57 1.80 2.10 0.74 0.70 0.52
GADD45A ENST00000370986 14.78 63.57 37.42 1.57 0.51 0.85 0.74 1.25 2.00
AKIRIN2 ENST00000257787 14.78 17.47 13.77 1.56 1.58 2.07 0.74 0.74 0.57
FAM19A1 ENST00000478136 14.79 38.57 24.74 1.56 0.72 1.05 0.74 1.67 1.10
ATPAF1 ENST00000576409 14.79 38.37 24.63 1.56 0.75 1.06 0.74 1.72 1.10
MCOLN1 ENST00000264079 14.80 32.01 21.53 1.56 0.92 1.28 0.74 1.48 0.92
ARHGEF3 ENST00000338458 14.80 24.71 17.65 1.56 1.30 1.66 0.74 1.05 0.78
AGPAT3 ENST00000398063 14.81 2.53 5.96 1.56 3.56 3.28 0.74 0.29 0.29
SESTD1 ENST00000428443 14.81 8.44 8.97 1.57 2.52 2.47 0.74 0.46 0.38
PLAG1 ENST00000316981 14.82 6.14 7.84 1.57 2.75 2.63 0.74 0.35 0.35
DCAF12 ENST00000361264 14.82 41.97 26.49 1.57 0.61 0.99 0.74 1.83 1.25
KCNA6 ENST00000433855 14.83 28.54 19.70 1.56 1.15 1.53 0.74 1.27 0.85
RNF8 ENST00000373479 14.83 4.60 7.06 1.56 3.24 2.88 0.74 0.32 0.33
SOX13 ENST00000367204 14.84 14.31 12.14 1.56 2.05 2.28 0.74 0.61 0.49
BAI1 ENST00000517894 14.84 2.69 6.03 1.56 3.52 3.29 0.74 0.29 0.30
RALGPS2 ENST00000367635 14.85 18.89 14.60 1.57 1.52 1.97 0.74 0.76 0.59

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