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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
TCEANC ENST00000314720 72.83 60.17 68.49 0.32 0.52 0.47 0.78 1.37 1.06
OR56B1 ENST00000317121 72.84 96.87 88.02 0.32 0.23 0.24 0.78 0.19 0.31
GLYATL3 ENST00000371197 72.84 76.31 77.77 0.32 0.43 0.38 0.78 0.86 0.55
OR9Q2 ENST00000311591 72.85 92.32 85.88 0.32 0.25 0.33 0.78 0.30 0.33
OR2J3 ENST00000377169 72.85 66.21 72.18 0.32 0.53 0.43 0.78 1.20 0.81
IAPP ENST00000240652 72.86 95.93 87.52 0.32 0.22 0.28 0.78 0.20 0.30
CASP6 ENST00000265164 72.86 61.45 69.29 0.32 0.54 0.43 0.78 1.40 0.98
SLC22A12 ENST00000377574 72.87 72.97 75.93 0.32 0.51 0.38 0.78 1.03 0.62
HIST1H2BH ENST00000356350 72.87 97.38 88.31 0.32 0.22 0.22 0.78 0.19 0.30
C12orf65 ENST00000253233 72.88 48.06 61.08 0.32 0.63 0.43 0.78 2.00 1.53
ZNF649 ENST00000354957 72.88 41.33 56.95 0.32 0.62 0.49 0.78 1.81 1.72
PDZD3 ENST00000355547 72.89 72.73 75.82 0.32 0.48 0.38 0.78 1.04 0.63
C4orf29 ENST00000398965 72.89 68.58 73.53 0.32 0.53 0.40 0.78 1.19 0.74
GPATCH11 ENST00000608836 72.90 61.69 69.45 0.32 0.56 0.44 0.78 1.39 0.98
S1PR4 ENST00000246115 72.90 69.82 74.19 0.32 0.54 0.39 0.78 1.14 0.69
TTC32 ENST00000333610 72.91 71.69 75.19 0.32 0.52 0.37 0.79 1.07 0.67
ZNF774 ENST00000354377 72.91 80.36 79.97 0.32 0.37 0.35 0.79 0.59 0.52
TP53INP2 ENST00000374810 72.92 28.08 49.38 0.32 1.19 0.70 0.79 1.20 1.84
EPCAM ENST00000263735 72.92 65.96 72.06 0.32 0.56 0.43 0.79 1.23 0.81
PAOX ENST00000278060 72.93 72.35 75.63 0.32 0.51 0.38 0.79 1.03 0.63
XIRP1 ENST00000340369 72.94 65.15 71.56 0.32 0.49 0.44 0.79 1.24 0.83
PBX4 ENST00000251203 72.94 56.69 66.48 0.32 0.53 0.51 0.79 1.55 1.21
CMPK2 ENST00000256722 72.95 77.20 78.32 0.32 0.43 0.38 0.79 0.78 0.54
NMUR1 ENST00000305141 72.95 71.58 75.19 0.32 0.53 0.38 0.79 1.07 0.67
FBRS ENST00000356166 72.96 1.19 35.28 0.32 4.01 0.86 0.79 0.28 1.76

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