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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
KIF17 ENST00000247986 53.08 52.49 51.97 0.63 0.66 0.62 1.78 1.83 1.92
KATNAL2 ENST00000245121 53.08 46.47 48.66 0.63 0.73 0.67 1.78 2.02 1.85
C9orf3 ENST00000375315 53.09 47.20 49.04 0.63 0.66 0.72 1.78 2.01 1.83
AARSD1 ENST00000427569 53.09 62.14 57.57 0.63 0.53 0.51 1.78 1.35 1.66
CCDC30 ENST00000428554 53.10 54.05 52.87 0.63 0.65 0.61 1.78 1.69 1.87
TERF2IP ENST00000300086 53.10 61.70 57.32 0.63 0.57 0.51 1.77 1.38 1.68
IL17B ENST00000261796 53.11 68.76 61.67 0.63 0.53 0.46 1.77 1.18 1.46
IRF2BPL ENST00000238647 53.11 14.37 31.95 0.63 2.04 0.91 1.77 0.61 1.57
AVPR2 ENST00000358927 53.12 43.23 46.89 0.63 0.62 0.68 1.76 1.92 1.88
GAB2 ENST00000361507 53.12 10.31 29.89 0.63 2.28 0.86 1.76 0.49 1.44
NLRC5 ENST00000262510 53.13 22.22 35.77 0.63 1.53 0.85 1.76 0.81 1.78
TNIP1 ENST00000389378 53.13 16.89 33.17 0.63 1.66 0.87 1.76 0.71 1.70
PEF1 ENST00000373703 53.14 61.42 57.18 0.63 0.54 0.52 1.76 1.39 1.70
DUSP5 ENST00000369583 53.14 49.83 50.52 0.63 0.66 0.67 1.76 2.02 1.86
ALDH9A1 ENST00000354775 53.15 63.10 58.18 0.63 0.48 0.48 1.76 1.29 1.65
AP1G2 ENST00000308724 53.15 69.87 62.35 0.63 0.54 0.48 1.76 1.15 1.41
FBXO7 ENST00000266087 53.16 47.31 49.15 0.63 0.67 0.73 1.76 2.00 1.83
TMEM74 ENST00000297459 53.16 76.80 66.69 0.63 0.42 0.54 1.76 0.81 1.20
DECR1 ENST00000220764 53.17 82.69 70.16 0.63 0.34 0.43 1.76 0.50 0.90
RIMBP2 ENST00000261655 53.17 14.78 32.20 0.63 1.96 0.91 1.75 0.62 1.60
VWF ENST00000261405 53.18 29.59 39.77 0.63 1.10 0.80 1.76 1.39 2.03
NDUFA12 ENST00000327772 53.18 78.37 67.60 0.63 0.43 0.51 1.75 0.74 1.12
THSD7B ENST00000272643 53.19 31.87 40.72 0.63 0.94 0.81 1.75 1.48 2.04
CNGA4 ENST00000379936 53.19 52.22 51.88 0.63 0.62 0.62 1.75 1.84 1.93
RTKN2 ENST00000373789 53.20 57.27 54.83 0.63 0.56 0.53 1.75 1.49 1.74

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