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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
CXorf36 ENST00000398000 63.92 73.93 71.43 0.58 0.53 0.46 1.21 1.02 0.87
TMEM18 ENST00000281017 63.93 72.75 70.67 0.58 0.48 0.43 1.21 1.04 0.88
MLF1 ENST00000392822 63.93 68.33 68.11 0.58 0.52 0.49 1.21 1.20 1.10
SELE ENST00000333360 63.94 46.91 55.02 0.58 0.71 0.51 1.21 1.94 1.73
PDGFB ENST00000331163 63.94 22.73 41.57 0.58 1.47 0.73 1.21 0.88 2.01
C19orf70 ENST00000309324 63.95 77.81 73.67 0.58 0.42 0.42 1.21 0.79 0.72
C5orf42 ENST00000425232 63.95 34.22 47.93 0.58 0.84 0.66 1.21 1.56 1.88
CTC-260F20.3 ENST00000555938 63.96 81.16 75.49 0.58 0.34 0.38 1.21 0.55 0.66
LDOC1L ENST00000341255 63.96 74.40 71.73 0.58 0.53 0.46 1.21 1.00 0.81
ARMC3 ENST00000298032 63.97 49.66 56.61 0.58 0.66 0.52 1.21 2.02 1.71
OR11A1 ENST00000377149 63.97 86.62 78.54 0.58 0.24 0.38 1.21 0.40 0.55
RECQL5 ENST00000317905 63.98 57.37 61.34 0.58 0.54 0.44 1.21 1.49 1.48
C10orf82 ENST00000369210 63.98 64.62 65.93 0.58 0.48 0.51 1.21 1.22 1.23
RP11-712L6.5 ENST00000524964 63.99 88.48 79.51 0.57 0.23 0.38 1.21 0.36 0.52
PRSS8 ENST00000317508 63.99 35.80 48.77 0.57 0.78 0.68 1.20 1.59 1.85
AHNAK ENST00000378024 64.00 12.97 36.62 0.57 2.07 0.85 1.20 0.59 1.92
RAB11FIP3 ENST00000262305 64.00 8.98 34.72 0.57 2.44 0.90 1.20 0.47 1.75
PCDHA4 ENST00000530339 64.01 81.95 75.99 0.57 0.35 0.38 1.20 0.50 0.62
PLSCR4 ENST00000354952 64.02 58.49 62.02 0.57 0.54 0.48 1.20 1.39 1.44
ST6GAL2 ENST00000409382 64.02 35.96 48.89 0.57 0.80 0.71 1.20 1.58 1.85
KRT80 ENST00000394815 64.03 41.60 52.05 0.57 0.63 0.62 1.20 1.80 1.93
PRND ENST00000305817 64.03 83.86 77.10 0.57 0.28 0.37 1.20 0.47 0.61
VWA3A ENST00000389398 64.04 49.86 56.78 0.57 0.66 0.52 1.20 2.02 1.70
MC4R ENST00000299766 64.04 83.18 76.71 0.57 0.28 0.34 1.20 0.48 0.61
SLC22A6 ENST00000377871 64.05 54.33 59.47 0.57 0.62 0.49 1.19 1.68 1.70

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