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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
C1orf50 ENST00000372525 58.24 52.13 54.78 0.56 0.61 0.54 1.53 1.85 1.74
USP50 ENST00000532404 58.25 91.66 78.18 0.56 0.24 0.39 1.53 0.32 0.55
COMMD10 ENST00000274458 58.25 92.37 78.57 0.56 0.25 0.38 1.53 0.30 0.55
SPR ENST00000234454 58.26 62.04 60.72 0.56 0.56 0.44 1.53 1.37 1.61
PNCK ENST00000447676 58.26 60.62 59.83 0.56 0.53 0.49 1.53 1.41 1.63
TECTB ENST00000369422 58.27 71.92 66.83 0.56 0.51 0.53 1.53 1.07 1.20
PCYOX1 ENST00000433351 58.27 77.36 70.05 0.56 0.42 0.47 1.53 0.76 0.91
SMTNL2 ENST00000389313 58.28 51.31 54.34 0.56 0.63 0.59 1.52 1.90 1.73
GPR75-ASB3 ENST00000352846 58.28 50.48 53.82 0.56 0.65 0.62 1.52 1.95 1.79
CCDC73 ENST00000335185 58.29 49.52 53.31 0.56 0.66 0.62 1.52 2.03 1.85
LPIN3 ENST00000373257 58.29 48.99 53.06 0.56 0.65 0.61 1.52 2.04 1.87
ZNF275 ENST00000370251 58.30 70.10 65.80 0.56 0.53 0.51 1.52 1.12 1.26
NRK ENST00000428173 58.30 10.43 32.57 0.56 2.23 0.89 1.52 0.50 1.63
ATG16L2 ENST00000321297 58.31 62.19 60.84 0.56 0.52 0.43 1.52 1.35 1.61
ABCG5 ENST00000260645 58.31 75.01 68.68 0.56 0.53 0.47 1.52 0.93 1.05
METTL7A ENST00000548553 58.32 72.43 67.12 0.56 0.49 0.51 1.52 1.03 1.17
GNG5 ENST00000370641 58.32 81.79 72.74 0.56 0.34 0.43 1.52 0.51 0.81
PLBD1 ENST00000240617 58.33 71.04 66.39 0.56 0.49 0.52 1.52 1.07 1.20
ADCK1 ENST00000238561 58.33 70.49 66.07 0.56 0.52 0.51 1.52 1.08 1.23
AGK ENST00000355413 58.34 48.28 52.61 0.56 0.63 0.61 1.53 2.01 1.89
KLKB1 ENST00000264690 58.34 54.53 56.17 0.56 0.59 0.49 1.52 1.65 1.77
ADAMTSL3 ENST00000286744 58.35 33.11 44.16 0.56 0.82 0.61 1.52 1.50 2.04
TRUB2 ENST00000372890 58.35 68.60 64.89 0.56 0.53 0.51 1.52 1.18 1.33
TM4SF4 ENST00000305354 58.36 81.91 72.87 0.56 0.35 0.40 1.52 0.51 0.81
TMEM27 ENST00000380342 58.36 88.64 76.61 0.56 0.24 0.37 1.52 0.35 0.60

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