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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
TAAR6 ENST00000275198 76.71 58.95 70.07 0.33 0.52 0.47 0.73 1.42 0.91
ABCA8 ENST00000269080 76.71 65.35 73.83 0.33 0.52 0.42 0.73 1.25 0.71
FAM151A ENST00000302250 76.72 81.20 82.34 0.33 0.35 0.33 0.73 0.55 0.44
B3GNT8 ENST00000321702 76.72 81.66 82.58 0.33 0.33 0.32 0.73 0.52 0.43
KLHDC7B ENST00000395676 76.73 78.58 80.99 0.33 0.40 0.39 0.73 0.74 0.50
GAST ENST00000329402 76.73 90.89 87.02 0.33 0.25 0.28 0.73 0.35 0.30
ALPK3 ENST00000258888 76.74 49.08 64.20 0.33 0.67 0.51 0.73 2.04 1.36
AMIGO3 ENST00000535833 76.74 71.64 77.37 0.33 0.53 0.35 0.73 1.07 0.58
RSPH3 ENST00000252655 76.75 44.98 61.58 0.33 0.68 0.46 0.73 1.97 1.48
CHRAC1 ENST00000220913 76.75 79.69 81.60 0.33 0.37 0.37 0.73 0.64 0.47
NUBP1 ENST00000283027 76.76 81.27 82.39 0.33 0.34 0.33 0.73 0.54 0.44
LMF1 ENST00000262301 76.76 68.10 75.35 0.33 0.52 0.37 0.73 1.20 0.65
TBC1D10C ENST00000312390 76.77 26.90 50.91 0.33 1.23 0.66 0.73 1.12 1.85
XCL1 ENST00000367818 76.77 95.21 89.12 0.33 0.23 0.19 0.73 0.21 0.26
C10orf113 ENST00000534331 76.78 92.05 87.55 0.33 0.24 0.27 0.73 0.33 0.30
SPATA21 ENST00000335496 76.78 79.31 81.39 0.33 0.38 0.37 0.73 0.67 0.49
AGBL4 ENST00000371839 76.79 38.83 57.82 0.33 0.68 0.51 0.73 1.66 1.66
RBM11 ENST00000400577 76.79 64.63 73.51 0.33 0.48 0.40 0.73 1.22 0.74
FAM167A ENST00000284486 76.80 97.22 90.09 0.33 0.24 0.18 0.73 0.19 0.22
LDHAL6A ENST00000280706 76.80 84.88 84.10 0.33 0.27 0.34 0.73 0.43 0.42
C14orf80 ENST00000392522 76.81 36.74 56.59 0.34 0.76 0.52 0.73 1.66 1.71
IQCJ ENST00000451172 76.81 70.92 77.00 0.34 0.49 0.37 0.73 1.07 0.61
RCN3 ENST00000270645 76.82 87.13 85.32 0.34 0.22 0.34 0.73 0.41 0.36
AFM ENST00000226355 76.82 72.82 78.01 0.34 0.49 0.38 0.73 1.04 0.54
EVC2 ENST00000344408 76.83 59.06 70.19 0.34 0.49 0.43 0.73 1.43 0.91

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