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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
TSR3 ENST00000007390 85.36 64.38 78.11 0.28 0.49 0.39 0.47 1.22 0.55
C6orf15 ENST00000259870 85.36 68.16 80.10 0.28 0.52 0.35 0.47 1.22 0.52
CCR10 ENST00000332438 85.37 73.08 82.62 0.28 0.53 0.32 0.47 1.02 0.43
KRTAP10-11 ENST00000334670 85.37 72.82 82.51 0.28 0.49 0.33 0.47 1.04 0.43
ZIM3 ENST00000269834 85.38 77.72 84.90 0.28 0.42 0.34 0.47 0.79 0.40
DHRS4L2 ENST00000335125 85.38 82.61 87.16 0.28 0.34 0.28 0.47 0.50 0.30
LCE2D ENST00000368784 85.39 94.02 92.39 0.28 0.25 0.14 0.47 0.26 0.15
AMH ENST00000221496 85.39 86.08 88.87 0.28 0.27 0.19 0.47 0.44 0.28
RSL1D1 ENST00000571133 85.40 52.64 71.54 0.28 0.68 0.44 0.47 1.81 0.83
OR4F5 ENST00000335137 85.40 91.19 91.23 0.28 0.23 0.15 0.47 0.35 0.18
OR52E6 ENST00000329322 85.41 81.43 86.62 0.28 0.33 0.30 0.47 0.54 0.33
DYNAP ENST00000321600 85.41 86.89 89.26 0.28 0.22 0.19 0.47 0.41 0.25
LRRC43 ENST00000339777 85.42 66.16 79.10 0.28 0.53 0.39 0.47 1.20 0.53
C11orf83 ENST00000531323 85.42 90.66 91.00 0.28 0.25 0.15 0.47 0.36 0.20
TPRX2P ENST00000535362 85.43 81.33 86.58 0.28 0.33 0.30 0.47 0.54 0.33
SPTSSA ENST00000298130 85.43 47.95 68.71 0.28 0.59 0.46 0.47 1.99 1.05
IRF7 ENST00000397566 85.44 82.23 87.04 0.28 0.34 0.28 0.47 0.52 0.30
DNMT3L ENST00000270172 85.44 71.37 81.79 0.28 0.53 0.37 0.47 1.05 0.47
TEX29 ENST00000283547 85.45 84.52 88.14 0.28 0.29 0.23 0.47 0.43 0.30
C14orf178 ENST00000355883 85.46 96.36 93.67 0.28 0.22 0.11 0.47 0.19 0.15
OR2A4 ENST00000315453 85.46 90.73 91.04 0.28 0.25 0.15 0.47 0.35 0.20
CXorf40B ENST00000370406 85.47 94.09 92.48 0.28 0.25 0.14 0.47 0.26 0.15
C12orf76 ENST00000309050 85.47 96.05 93.51 0.28 0.21 0.11 0.47 0.20 0.15
KRTAP13-3 ENST00000390690 85.48 94.10 92.51 0.28 0.25 0.14 0.47 0.26 0.15
ZNRF4 ENST00000222033 85.48 77.55 84.88 0.28 0.42 0.34 0.47 0.79 0.40

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