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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
FAM166A ENST00000344774 79.55 81.73 83.92 0.34 0.33 0.35 0.57 0.52 0.43
MB21D1 ENST00000370315 79.55 71.70 78.89 0.33 0.52 0.39 0.58 1.07 0.52
KRTAP5-3 ENST00000399685 79.56 84.56 85.41 0.33 0.29 0.34 0.58 0.42 0.35
COX7A2 ENST00000370081 79.56 74.94 80.58 0.33 0.53 0.39 0.58 0.94 0.52
C7orf57 ENST00000348904 79.57 82.83 84.56 0.33 0.32 0.34 0.58 0.50 0.40
USP6NL ENST00000277575 79.57 18.26 47.75 0.33 1.48 0.65 0.58 0.74 1.88
MUM1 ENST00000344663 79.58 27.66 53.03 0.33 1.27 0.61 0.58 1.18 1.86
TRO ENST00000173898 79.58 43.83 62.63 0.33 0.61 0.48 0.58 1.95 1.40
LY86 ENST00000379953 79.59 87.35 86.66 0.33 0.22 0.30 0.58 0.41 0.33
DNAH6 ENST00000389394 79.59 29.22 53.85 0.33 1.13 0.62 0.58 1.35 1.78
PPP1R3D ENST00000370996 79.60 87.53 86.74 0.33 0.23 0.30 0.57 0.37 0.32
VWA5A ENST00000456829 79.60 76.26 81.29 0.33 0.44 0.38 0.57 0.86 0.48
MAMDC4 ENST00000317446 79.61 72.33 79.27 0.33 0.51 0.38 0.57 1.03 0.54
OR52E8 ENST00000537935 79.61 63.13 74.23 0.33 0.47 0.39 0.57 1.30 0.69
GATA5 ENST00000252997 79.62 26.05 52.07 0.33 1.20 0.61 0.58 1.10 1.92
DISC1 ENST00000366633 79.62 42.00 61.50 0.33 0.59 0.44 0.58 1.84 1.48
NANOS2 ENST00000341294 79.63 86.22 86.16 0.33 0.27 0.33 0.58 0.43 0.33
TMEM44 ENST00000392432 79.63 78.75 82.58 0.33 0.42 0.32 0.57 0.72 0.43
PTGDS ENST00000371625 79.64 46.26 64.23 0.33 0.73 0.51 0.57 2.04 1.35
CYP2F1 ENST00000331105 79.64 67.52 76.68 0.33 0.54 0.35 0.57 1.20 0.60
FCRL1 ENST00000368176 79.65 49.28 66.13 0.33 0.65 0.52 0.57 2.02 1.21
SLFNL1 ENST00000359345 79.65 60.82 72.99 0.33 0.56 0.40 0.57 1.40 0.80
OR9G1 ENST00000312153 79.66 87.86 86.96 0.33 0.24 0.28 0.57 0.38 0.30
MPND ENST00000262966 79.67 49.27 66.12 0.33 0.65 0.51 0.57 2.03 1.21
GAS2L1 ENST00000341313 79.67 23.25 50.47 0.33 1.43 0.67 0.57 0.92 1.87

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