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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
AP2A1 ENST00000359032 12.66 1.22 4.21 1.68 4.01 3.77 0.66 0.27 0.24
GNE ENST00000396594 12.66 65.39 37.33 1.68 0.53 0.84 0.66 1.25 2.01
MET ENST00000318493 12.67 11.41 9.48 1.68 2.10 2.30 0.66 0.56 0.40
ASH1L ENST00000392403 12.67 0.25 3.83 1.68 4.12 3.77 0.66 0.28 0.24
EPC2 ENST00000258484 12.68 3.47 5.37 1.68 3.39 3.50 0.65 0.29 0.25
KIAA0430 ENST00000396368 12.69 1.83 4.58 1.68 3.78 3.70 0.65 0.26 0.25
CPEB1 ENST00000568128 12.69 6.76 7.08 1.68 2.67 2.86 0.65 0.37 0.33
ESPL1 ENST00000257934 12.70 3.69 5.52 1.68 3.34 3.42 0.65 0.31 0.26
RPL3 ENST00000216146 12.70 8.28 7.85 1.67 2.54 2.63 0.65 0.45 0.35
EWSR1 ENST00000414183 12.71 3.07 5.17 1.67 3.47 3.61 0.65 0.28 0.25
HTATSF1 ENST00000535601 12.71 7.19 7.36 1.67 2.58 2.78 0.65 0.37 0.34
ANO4 ENST00000392979 12.72 20.46 14.31 1.67 1.43 2.00 0.65 0.76 0.60
RAB24 ENST00000303251 12.72 32.53 20.76 1.67 0.86 1.46 0.65 1.49 0.89
PUM2 ENST00000338086 12.73 11.46 9.56 1.67 2.11 2.29 0.65 0.56 0.40
OXSR1 ENST00000311806 12.73 14.77 11.43 1.67 1.96 2.19 0.65 0.62 0.45
TMEM115 ENST00000266025 12.74 24.46 16.40 1.67 1.32 1.71 0.65 1.00 0.68
VBP1 ENST00000286428 12.74 23.52 15.97 1.67 1.39 1.77 0.65 0.92 0.66
LRRC8B ENST00000330947 12.75 8.82 8.16 1.67 2.47 2.59 0.65 0.48 0.37
ZDHHC22 ENST00000319374 12.75 60.22 34.73 1.67 0.53 0.90 0.65 1.39 1.75
CALCRL ENST00000409998 12.76 12.41 10.13 1.67 2.06 2.24 0.65 0.59 0.41
UBL3 ENST00000380680 12.76 27.99 18.33 1.68 1.20 1.66 0.65 1.18 0.80
ESRRB ENST00000380887 12.77 26.50 17.50 1.68 1.18 1.62 0.65 1.11 0.75
HSF5 ENST00000323777 12.77 7.08 7.28 1.68 2.57 2.80 0.65 0.37 0.34
PSMD7 ENST00000219313 12.78 28.41 18.55 1.68 1.16 1.61 0.65 1.24 0.81
CSRNP2 ENST00000228515 12.78 14.53 11.33 1.68 2.04 2.19 0.66 0.61 0.45

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