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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
SCOC ENST00000608372 67.15 66.57 68.89 0.61 0.56 0.46 1.04 1.21 1.04
BAIAP2L2 ENST00000381669 67.16 60.98 65.66 0.61 0.54 0.51 1.05 1.41 1.29
PQLC1 ENST00000397778 67.16 50.97 59.31 0.61 0.65 0.51 1.05 1.92 1.69
LYSMD2 ENST00000267838 67.17 50.22 58.80 0.61 0.67 0.51 1.05 1.99 1.65
GPT ENST00000394955 67.17 81.88 77.73 0.61 0.35 0.38 1.05 0.51 0.55
OLFML2B ENST00000294794 67.18 55.50 62.14 0.61 0.56 0.48 1.05 1.61 1.44
KLHL25 ENST00000337975 67.18 96.00 84.96 0.61 0.22 0.33 1.05 0.20 0.40
RPUSD4 ENST00000298317 67.19 65.24 68.20 0.59 0.51 0.49 1.05 1.24 1.08
MFSD2B ENST00000406420 67.19 64.65 67.82 0.59 0.48 0.51 1.05 1.24 1.12
OCA2 ENST00000354638 67.20 42.81 54.59 0.59 0.63 0.56 1.04 1.92 1.74
ENDOD1 ENST00000278505 67.20 84.54 79.20 0.59 0.29 0.38 1.03 0.42 0.54
DECR2 ENST00000219481 67.21 85.68 79.75 0.59 0.27 0.38 1.03 0.44 0.53
A4GALT ENST00000401850 67.21 84.97 79.38 0.59 0.25 0.39 1.03 0.45 0.52
NDUFC2-KCTD14 ENST00000530054 67.22 45.67 56.21 0.59 0.75 0.49 1.03 2.01 1.77
ZNF461 ENST00000588268 67.22 55.65 62.26 0.59 0.53 0.48 1.03 1.60 1.43
PI16 ENST00000373674 67.23 72.26 72.44 0.59 0.51 0.44 1.03 1.03 0.83
MRPS12 ENST00000407800 67.23 93.25 83.64 0.59 0.28 0.33 1.03 0.30 0.40
PHLDA3 ENST00000367311 67.24 72.05 72.34 0.59 0.52 0.44 1.03 1.03 0.82
PYROXD1 ENST00000240651 67.24 53.18 60.79 0.59 0.66 0.43 1.03 1.75 1.61
NUP62CL ENST00000372466 67.25 78.55 75.91 0.59 0.40 0.38 1.04 0.73 0.62
LYRM1 ENST00000396052 67.25 95.06 84.51 0.59 0.23 0.33 1.04 0.21 0.40
CYB5B ENST00000307892 67.26 46.71 56.84 0.59 0.73 0.52 1.04 1.97 1.70
DNAJC25-GNG10 ENST00000374294 67.26 92.45 83.23 0.59 0.27 0.29 1.05 0.30 0.40
NOP14 ENST00000416614 67.27 29.75 47.25 0.59 1.13 0.66 1.05 1.40 1.87
INSC ENST00000379554 67.27 72.92 72.82 0.59 0.49 0.43 1.05 1.02 0.81

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