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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
PHGR1 ENST00000448599 89.75 88.70 93.46 0.16 0.25 0.11 0.28 0.35 0.15
PGA4 ENST00000378149 89.75 92.97 96.03 0.16 0.29 0.07 0.28 0.30 0.11
CCDC85B ENST00000312579 89.76 63.99 80.23 0.16 0.48 0.37 0.28 1.20 0.51
TMEM30C ENST00000429523 89.76 63.16 79.80 0.16 0.47 0.38 0.28 1.31 0.52
RIIAD1 ENST00000479191 89.77 94.74 95.04 0.16 0.23 0.09 0.28 0.24 0.10
RP11-542P2.1 ENST00000503109 89.77 68.69 84.72 0.16 0.53 0.34 0.28 1.17 0.40
RP11-1026M7.2 ENST00000502515 89.78 92.03 93.72 0.16 0.24 0.10 0.28 0.33 0.14
FAM25C ENST00000342763 89.78 94.11 94.71 0.16 0.25 0.09 0.28 0.25 0.11
SPG20OS ENST00000379848 89.79 94.24 94.76 0.16 0.24 0.09 0.28 0.25 0.11
TREX2 ENST00000330912 89.79 82.67 90.84 0.16 0.34 0.15 0.28 0.50 0.20
CDRT15L2 ENST00000399044 89.80 90.22 92.79 0.16 0.25 0.14 0.28 0.38 0.15
PAXIP1-AS2 ENST00000397551 89.80 66.51 81.56 0.16 0.57 0.35 0.28 1.22 0.48
AC009403.2 ENST00000401694 89.81 93.11 95.07 0.16 0.28 0.09 0.28 0.30 0.10
C6orf52 ENST00000259983 89.81 86.07 90.97 0.16 0.27 0.15 0.28 0.44 0.20
TDRD15 ENST00000405799 89.82 26.19 60.41 0.16 1.19 0.44 0.28 1.08 1.58
C6orf99 ENST00000367072 89.82 79.74 88.82 0.16 0.37 0.19 0.28 0.64 0.28
GRAPL ENST00000344415 89.83 92.86 94.14 0.16 0.29 0.09 0.28 0.30 0.12
RP11-826N14.2 ENST00000512675 89.84 92.21 93.84 0.16 0.25 0.10 0.28 0.31 0.13
CTC-236F12.4 ENST00000506836 89.84 91.42 93.45 0.16 0.23 0.11 0.28 0.33 0.15
NPIPA1 ENST00000328085 89.85 91.58 93.52 0.16 0.23 0.13 0.28 0.33 0.15
HIST1H4K ENST00000357549 89.85 97.09 96.26 0.16 0.24 0.07 0.28 0.19 0.09
RP11-865B13.1 ENST00000584361 89.86 50.93 73.18 0.16 0.65 0.43 0.28 1.94 0.79
C8orf87 ENST00000521906 89.86 86.35 91.11 0.16 0.25 0.15 0.28 0.43 0.19
TPRXL ENST00000424053 89.87 97.65 96.64 0.16 0.21 0.08 0.28 0.19 0.08
AC016586.1 ENST00000535853 89.87 97.66 96.65 0.16 0.21 0.08 0.28 0.19 0.08

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