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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
SAMD7 ENST00000428432 74.64 60.14 69.58 0.38 0.52 0.44 0.78 1.39 0.95
SYCP2 ENST00000357552 74.64 3.98 37.58 0.38 3.27 0.84 0.78 0.32 2.01
STX10 ENST00000587230 74.65 78.20 79.72 0.38 0.43 0.38 0.78 0.74 0.53
TNFSF14 ENST00000599359 74.66 44.22 59.80 0.38 0.62 0.49 0.78 1.95 1.64
LTB4R2 ENST00000543919 74.66 70.09 75.28 0.38 0.53 0.37 0.78 1.13 0.66
ZNF750 ENST00000269394 74.67 18.87 45.48 0.38 1.53 0.70 0.78 0.75 1.98
ABI3 ENST00000225941 74.67 47.81 62.00 0.38 0.59 0.49 0.78 1.99 1.45
TMC3 ENST00000359440 74.68 52.59 65.06 0.38 0.67 0.51 0.78 1.82 1.31
GP2 ENST00000381362 74.68 75.60 78.38 0.38 0.44 0.38 0.78 0.90 0.54
OR5R1 ENST00000312253 74.69 88.37 84.89 0.38 0.23 0.34 0.78 0.37 0.40
ITLN1 ENST00000326245 74.69 60.11 69.59 0.38 0.52 0.44 0.78 1.39 0.95
AVEN ENST00000306730 74.70 76.58 78.90 0.38 0.42 0.39 0.78 0.83 0.52
ARHGAP11B ENST00000428041 74.70 81.80 81.64 0.38 0.34 0.37 0.78 0.51 0.47
MIOX ENST00000216075 74.71 87.80 84.60 0.38 0.24 0.34 0.78 0.37 0.40
MSRB1 ENST00000361871 74.71 63.71 71.76 0.38 0.49 0.46 0.78 1.23 0.81
KLF15 ENST00000296233 74.72 32.38 52.85 0.38 0.87 0.61 0.78 1.47 1.88
FAS ENST00000355740 74.72 20.50 46.27 0.38 1.43 0.67 0.78 0.78 1.92
ADH4 ENST00000265512 74.73 70.94 75.84 0.38 0.49 0.38 0.78 1.05 0.63
HMGN1 ENST00000380749 74.73 48.57 62.52 0.38 0.65 0.48 0.78 2.01 1.39
ACOT1 ENST00000311148 74.74 70.75 75.74 0.38 0.48 0.38 0.78 1.08 0.64
OR5D18 ENST00000333976 74.74 88.59 85.02 0.38 0.24 0.33 0.78 0.35 0.39
DGAT2L6 ENST00000333026 74.75 88.19 84.84 0.38 0.23 0.34 0.78 0.38 0.40
SQSTM1 ENST00000389805 74.75 40.12 57.35 0.38 0.63 0.51 0.78 1.71 1.67
IFITM1 ENST00000408968 74.76 89.70 85.60 0.38 0.27 0.32 0.78 0.37 0.35
COX8A ENST00000314133 74.76 92.42 86.76 0.38 0.27 0.30 0.78 0.30 0.31

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