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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
MCCC2 ENST00000340941 53.59 47.65 49.55 0.62 0.61 0.67 1.76 1.97 1.84
PIGV ENST00000374145 53.60 67.00 60.91 0.62 0.53 0.43 1.76 1.25 1.58
ARMC9 ENST00000349938 53.60 55.39 53.99 0.62 0.58 0.61 1.77 1.60 1.77
NSRP1 ENST00000247026 53.61 29.65 39.97 0.62 1.10 0.81 1.77 1.39 1.99
USH1G ENST00000319642 53.61 59.20 56.14 0.62 0.49 0.49 1.77 1.44 1.77
LOXL2 ENST00000389131 53.62 31.78 40.90 0.62 0.94 0.78 1.77 1.48 2.06
ACTR1B ENST00000289228 53.62 36.22 43.29 0.62 0.82 0.63 1.77 1.61 2.01
HIST1H2BB ENST00000357905 53.63 94.82 77.42 0.62 0.23 0.35 1.76 0.24 0.57
CPA4 ENST00000222482 53.63 76.90 67.01 0.62 0.43 0.52 1.76 0.79 1.19
ITGA8 ENST00000378076 53.64 34.40 42.24 0.62 0.84 0.70 1.76 1.56 2.01
UROS ENST00000368797 53.64 41.89 46.42 0.62 0.61 0.67 1.76 1.82 1.91
ZNF568 ENST00000333987 53.65 51.27 51.60 0.62 0.65 0.62 1.76 1.90 1.94
MYO1A ENST00000442789 53.65 72.68 64.46 0.62 0.47 0.51 1.76 1.04 1.33
HNMT ENST00000280097 53.66 42.34 46.72 0.62 0.61 0.66 1.76 1.90 1.87
SDHD ENST00000375549 53.66 49.14 50.45 0.62 0.66 0.67 1.76 2.04 1.88
C4B ENST00000435363 53.67 21.12 35.55 0.62 1.47 0.85 1.76 0.82 1.78
PACRGL ENST00000503585 53.67 86.10 72.56 0.63 0.27 0.46 1.76 0.44 0.82
ANXA1 ENST00000376911 53.68 55.77 54.27 0.63 0.52 0.59 1.77 1.58 1.73
PCDHGA9 ENST00000573521 53.69 43.37 47.28 0.63 0.59 0.67 1.77 1.95 1.87
RRN3 ENST00000198767 53.69 33.97 42.04 0.63 0.84 0.70 1.77 1.55 1.98
LRCH4 ENST00000310300 53.70 36.90 43.65 0.63 0.76 0.59 1.78 1.70 2.02
BCL2L11 ENST00000393256 53.70 20.16 35.12 0.63 1.43 0.86 1.78 0.75 1.77
MRAP2 ENST00000257776 53.71 91.78 75.75 0.63 0.23 0.38 1.78 0.32 0.64
KRT4 ENST00000551956 53.71 57.40 55.14 0.63 0.54 0.51 1.77 1.49 1.74
AIF1 ENST00000376059 53.72 82.33 70.31 0.63 0.34 0.43 1.77 0.53 0.90

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