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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
RAB26 ENST00000210187 79.18 86.47 86.06 0.33 0.24 0.33 0.61 0.42 0.33
PSMD5 ENST00000210313 38.68 54.01 44.99 0.92 0.65 0.68 1.74 1.69 2.04
NANS ENST00000210444 49.26 72.97 61.86 0.57 0.51 0.47 1.80 1.03 1.46
SEMA4G ENST00000210633 40.88 41.69 39.64 0.84 0.61 0.80 1.73 1.80 2.04
TPSD1 ENST00000211076 86.02 91.05 91.44 0.25 0.25 0.15 0.44 0.36 0.18
GSTA3 ENST00000211122 79.94 61.03 73.25 0.30 0.54 0.43 0.59 1.39 0.79
MAPK13 ENST00000211287 48.32 59.55 53.33 0.56 0.51 0.62 1.81 1.40 1.86
TMEM14A ENST00000211314 34.50 76.85 55.28 1.00 0.42 0.51 1.80 0.81 1.73
PRRT1 ENST00000211413 3.66 41.18 20.55 3.80 0.59 1.48 0.31 1.82 0.89
ZNF184 ENST00000211936 18.69 27.74 21.31 1.53 1.25 1.39 0.90 1.19 0.91
VCL ENST00000211998 7.66 17.86 10.32 2.72 1.51 2.19 0.40 0.72 0.43
SIRT1 ENST00000212015 25.45 25.57 23.62 1.35 1.25 1.19 1.17 1.05 1.01
TGFBR3 ENST00000212355 29.24 24.50 24.92 1.10 1.32 1.02 1.56 1.01 1.11
TMED1 ENST00000214869 66.30 87.26 80.11 0.58 0.22 0.35 1.07 0.41 0.52
MZF1 ENST00000215057 82.18 59.53 73.61 0.30 0.49 0.40 0.57 1.41 0.74
OCEL1 ENST00000215061 82.70 64.87 76.92 0.30 0.48 0.35 0.57 1.24 0.60
PSMD8 ENST00000215071 46.12 32.18 37.41 0.58 0.87 0.85 1.81 1.46 2.00
STX1B ENST00000215095 4.37 11.40 5.16 3.72 2.10 3.61 0.30 0.56 0.25
BCL7C ENST00000215115 35.96 43.45 37.94 0.94 0.61 0.85 1.87 1.95 2.02
EFNA2 ENST00000215368 87.71 66.85 80.61 0.23 0.53 0.39 0.37 1.24 0.52
ATP5D ENST00000215375 83.79 78.46 84.47 0.29 0.43 0.33 0.49 0.74 0.40
AMELY ENST00000215479 93.17 96.57 97.59 0.15 0.22 0.09 0.16 0.19 0.06
FGF22 ENST00000215530 83.92 95.41 92.35 0.29 0.24 0.14 0.48 0.21 0.15
C19orf77 ENST00000215531 90.87 77.95 87.78 0.16 0.42 0.24 0.20 0.79 0.32
NDUFB7 ENST00000215565 82.02 86.03 87.20 0.30 0.25 0.28 0.57 0.43 0.31

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