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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
USP45 ENST00000327681 57.98 55.64 56.62 0.56 0.53 0.52 1.52 1.60 1.72
TMEM132A ENST00000005286 57.99 42.77 49.28 0.56 0.62 0.70 1.52 1.91 1.85
PIWIL4 ENST00000299001 57.99 29.83 42.16 0.56 1.13 0.68 1.52 1.40 2.01
TRUB1 ENST00000298746 58.00 61.09 59.96 0.56 0.53 0.49 1.52 1.39 1.61
GPRC5C ENST00000392627 58.00 48.39 52.52 0.56 0.63 0.61 1.52 2.00 1.90
EML2 ENST00000587152 58.01 55.89 56.78 0.56 0.51 0.52 1.52 1.57 1.70
TSGA13 ENST00000456951 58.01 80.89 72.07 0.56 0.35 0.43 1.52 0.57 0.81
TMEM38B ENST00000374692 58.02 45.87 51.01 0.56 0.75 0.66 1.52 2.02 1.87
TMEM161A ENST00000162044 58.02 44.04 50.02 0.56 0.61 0.61 1.53 1.97 1.92
NDUFAF1 ENST00000260361 58.03 48.90 52.79 0.56 0.63 0.61 1.53 2.04 1.88
HOXD12 ENST00000406506 58.03 78.96 70.84 0.57 0.40 0.43 1.53 0.69 0.86
SLC8B1 ENST00000552014 58.04 67.04 63.80 0.57 0.54 0.49 1.53 1.24 1.38
MYLK3 ENST00000394809 58.04 37.71 46.54 0.57 0.78 0.66 1.53 1.70 1.90
ADCK3 ENST00000366779 58.05 55.90 56.82 0.57 0.51 0.52 1.53 1.56 1.70
PDZD7 ENST00000370215 58.05 65.72 62.87 0.57 0.53 0.51 1.53 1.22 1.40
ADAMTS17 ENST00000268070 58.06 38.58 47.04 0.57 0.72 0.68 1.53 1.67 1.88
COL4A6 ENST00000372216 58.07 14.53 34.51 0.57 2.04 0.90 1.53 0.61 1.77
CYC1 ENST00000318911 58.07 32.12 43.46 0.57 0.89 0.62 1.54 1.46 2.01
ERI2 ENST00000357967 58.08 54.78 56.15 0.57 0.57 0.49 1.54 1.63 1.77
ERMAP ENST00000372517 58.08 67.22 63.93 0.57 0.54 0.51 1.54 1.22 1.38
ALDH1B1 ENST00000377698 58.09 72.78 67.21 0.57 0.49 0.52 1.54 1.04 1.16
PCDHGA11 ENST00000398587 58.09 49.82 53.35 0.57 0.66 0.62 1.54 2.02 1.85
EEF2K ENST00000263026 58.10 59.64 58.97 0.57 0.52 0.49 1.54 1.40 1.65
AK4 ENST00000395334 58.10 37.68 46.55 0.57 0.78 0.66 1.54 1.70 1.90
MRPS15 ENST00000373116 58.11 78.77 70.77 0.57 0.42 0.43 1.54 0.71 0.86

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