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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
KLHDC8B ENST00000332780 20.92 58.55 37.99 1.54 0.54 0.85 1.02 1.41 2.03
TESK1 ENST00000336395 20.93 12.01 14.17 1.54 2.07 2.00 1.02 0.57 0.60
IMPACT ENST00000284202 20.93 62.86 40.18 1.54 0.51 0.82 1.02 1.29 1.99
KIF4A ENST00000374403 20.94 5.71 10.94 1.54 2.92 2.23 1.02 0.34 0.44
FAM105B ENST00000284274 20.94 29.52 23.37 1.54 1.10 1.19 1.02 1.39 0.99
OSER1 ENST00000372970 20.95 51.42 34.44 1.54 0.63 0.90 1.01 1.90 1.76
LRRTM1 ENST00000295057 20.95 24.39 20.83 1.53 1.29 1.46 1.01 1.00 0.88
RAD23A ENST00000586534 20.96 27.04 22.10 1.54 1.23 1.15 1.01 1.12 0.96
FBXL2 ENST00000484457 20.96 26.83 22.01 1.54 1.23 1.18 1.01 1.12 0.97
NEXN ENST00000334785 20.97 41.12 29.18 1.54 0.59 0.84 1.01 1.82 1.33
STRN3 ENST00000357479 20.98 15.69 16.13 1.54 1.87 1.71 1.01 0.68 0.66
ZNF513 ENST00000323703 20.98 19.57 18.23 1.54 1.43 1.64 1.01 0.74 0.79
ZNF319 ENST00000299237 20.99 3.09 9.47 1.54 3.46 2.30 1.01 0.28 0.40
USP21 ENST00000368002 20.99 27.38 22.37 1.54 1.25 1.16 1.01 1.17 0.97
KLF1 ENST00000264834 21.00 52.10 34.76 1.54 0.61 0.90 1.01 1.85 1.76
RAB3IP ENST00000550536 21.00 48.15 32.76 1.54 0.63 0.86 1.01 1.97 1.65
ADAM22 ENST00000265727 21.01 16.61 16.68 1.54 1.73 1.70 1.01 0.71 0.70
LPHN1 ENST00000340736 21.01 4.43 10.28 1.54 3.28 2.21 1.01 0.32 0.42
YOD1 ENST00000315927 21.02 40.32 28.81 1.54 0.62 0.80 1.02 1.74 1.32
SLC25A51 ENST00000377716 21.02 65.11 41.29 1.54 0.51 0.75 1.02 1.24 2.01
CRABP1 ENST00000299529 21.03 76.38 47.47 1.54 0.43 0.63 1.02 0.86 1.89
MAG ENST00000392213 21.03 19.96 18.44 1.54 1.47 1.62 1.02 0.73 0.81
EIF2B1 ENST00000424014 21.04 48.35 32.86 1.54 0.63 0.85 1.02 2.00 1.66
HOMEZ ENST00000357460 21.04 31.56 24.36 1.54 0.95 1.09 1.02 1.43 1.07
RASGEF1B ENST00000264400 21.05 15.87 16.26 1.54 1.89 1.70 1.02 0.68 0.65

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