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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
HRASLS2 ENST00000255695 97.28 90.74 96.81 0.10 0.25 0.08 0.11 0.35 0.07
ZNF506 ENST00000443905 96.68 84.83 93.49 0.11 0.27 0.11 0.11 0.42 0.15
SMR3A ENST00000226460 96.09 86.64 94.12 0.11 0.24 0.09 0.11 0.40 0.12
PSG4 ENST00000405312 96.10 96.77 98.61 0.11 0.23 0.10 0.11 0.19 0.05
DIRC1 ENST00000308100 96.69 99.86 99.44 0.11 0.17 0.11 0.11 0.11 0.05
LRRC27 ENST00000368614 97.28 74.41 88.97 0.10 0.53 0.19 0.11 1.00 0.28
OR14C36 ENST00000317861 97.88 98.68 99.64 0.11 0.18 0.12 0.11 0.15 0.04
RAET1G ENST00000367360 98.47 76.00 90.27 0.10 0.43 0.16 0.11 0.86 0.22
NACAD ENST00000490531 96.10 17.97 56.88 0.11 1.53 0.51 0.11 0.73 1.70
BCL2L10 ENST00000260442 96.69 87.46 94.80 0.11 0.23 0.09 0.11 0.40 0.11
OR2T3 ENST00000359594 97.29 99.76 99.38 0.10 0.17 0.11 0.11 0.11 0.04
AL583828.1 ENST00000558378 97.88 99.57 99.52 0.11 0.16 0.12 0.11 0.12 0.05
IVL ENST00000368764 98.48 99.18 99.85 0.10 0.15 0.12 0.11 0.13 0.04
ZNF707 ENST00000532205 96.11 61.64 82.25 0.11 0.54 0.35 0.11 1.39 0.44
VSTM1 ENST00000338372 96.70 77.24 90.05 0.11 0.43 0.18 0.11 0.78 0.22
CMTM1 ENST00000379500 97.29 71.23 87.41 0.10 0.53 0.28 0.11 1.06 0.31
H2BFWT ENST00000217926 97.89 87.84 95.64 0.11 0.24 0.08 0.11 0.38 0.11
OR14A16 ENST00000357627 98.48 99.12 99.68 0.10 0.15 0.12 0.11 0.14 0.04
ZNF77 ENST00000314531 96.11 80.86 91.39 0.11 0.35 0.15 0.11 0.57 0.18
C7orf33 ENST00000307003 96.70 92.13 97.16 0.11 0.24 0.08 0.11 0.32 0.07
ZNF765 ENST00000396408 97.30 96.74 98.98 0.10 0.23 0.11 0.11 0.19 0.04
CD163L1 ENST00000313599 97.89 46.82 75.26 0.11 0.71 0.37 0.11 1.97 0.67
KRTAP19-1 ENST00000390689 96.12 99.94 99.14 0.11 0.17 0.11 0.11 0.10 0.04
GSDMD ENST00000526406 98.49 75.44 90.06 0.10 0.46 0.18 0.11 0.90 0.22
TMEM105 ENST00000332900 96.71 95.91 98.53 0.11 0.22 0.10 0.11 0.20 0.05

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