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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
LAYN ENST00000375615 59.53 71.82 67.48 0.57 0.51 0.52 1.41 1.07 1.14
MRPS18B ENST00000259873 59.54 60.94 60.82 0.57 0.54 0.43 1.41 1.41 1.61
C12orf10 ENST00000267103 59.54 70.94 66.97 0.57 0.49 0.53 1.41 1.05 1.19
FAIM ENST00000338446 59.55 74.88 69.35 0.57 0.53 0.43 1.41 0.95 0.98
MOXD1 ENST00000367963 59.55 77.57 70.94 0.57 0.42 0.43 1.42 0.79 0.86
GCC2 ENST00000309863 59.56 19.19 37.64 0.57 1.48 0.82 1.42 0.76 2.01
FAM181A ENST00000267594 59.56 70.23 66.56 0.57 0.52 0.52 1.42 1.12 1.20
KLK11 ENST00000594768 59.57 53.48 56.29 0.57 0.65 0.49 1.43 1.71 1.75
CKLF ENST00000264001 59.57 78.19 71.38 0.57 0.43 0.44 1.43 0.73 0.86
ANXA13 ENST00000262219 59.58 58.58 59.30 0.57 0.54 0.51 1.43 1.41 1.68
SNRNP48 ENST00000342415 59.58 58.96 59.59 0.57 0.52 0.49 1.43 1.43 1.69
AUNIP ENST00000374298 59.59 84.31 74.86 0.57 0.28 0.39 1.43 0.44 0.64
HTR3C ENST00000318351 59.59 73.14 68.33 0.57 0.53 0.49 1.43 1.02 1.07
CYSLTR2 ENST00000282018 59.60 87.41 76.59 0.57 0.23 0.37 1.42 0.40 0.61
ENKUR ENST00000331161 59.60 66.20 64.19 0.57 0.53 0.51 1.42 1.21 1.36
BLK ENST00000259089 59.61 65.21 63.61 0.57 0.51 0.49 1.42 1.23 1.39
SPRY1 ENST00000394339 59.61 66.79 64.53 0.57 0.56 0.51 1.41 1.23 1.34
FGF20 ENST00000180166 59.62 27.81 41.96 0.57 1.23 0.68 1.41 1.19 2.01
D2HGDH ENST00000321264 59.63 29.69 43.02 0.57 1.11 0.67 1.40 1.39 2.01
RNF126 ENST00000292363 59.63 14.67 35.36 0.57 2.00 0.87 1.40 0.62 1.77
LECT1 ENST00000377962 59.64 64.91 63.44 0.57 0.48 0.51 1.39 1.25 1.38
ABHD14A-ACY1 ENST00000463937 59.64 59.35 59.90 0.57 0.51 0.49 1.40 1.41 1.63
MRPS17 ENST00000426595 59.65 81.19 73.15 0.57 0.35 0.43 1.39 0.55 0.79
HUS1 ENST00000258774 59.65 62.97 62.11 0.57 0.51 0.48 1.39 1.31 1.44
MDM1 ENST00000303145 59.66 49.10 53.82 0.57 0.66 0.62 1.39 2.04 1.79

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