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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
PCDHGB6 ENST00000520790 57.85 42.49 49.08 0.57 0.59 0.72 1.54 1.88 1.82
ZNF660 ENST00000322734 57.86 86.39 75.05 0.57 0.25 0.39 1.54 0.42 0.66
HTR5A ENST00000287907 57.86 54.93 56.13 0.57 0.57 0.49 1.54 1.63 1.77
MAN2C1 ENST00000565683 57.87 61.04 59.79 0.57 0.54 0.49 1.55 1.39 1.64
AMACR ENST00000382085 57.87 42.83 49.24 0.57 0.63 0.72 1.54 1.91 1.85
SLC46A3 ENST00000380814 57.88 63.58 61.41 0.57 0.51 0.44 1.53 1.25 1.48
PROK2 ENST00000295619 57.88 86.12 74.93 0.56 0.27 0.39 1.53 0.43 0.64
KCNA7 ENST00000221444 57.89 40.30 47.94 0.56 0.62 0.66 1.53 1.75 1.88
IL21R ENST00000337929 57.89 6.70 30.55 0.56 2.66 0.80 1.53 0.37 1.47
GPR152 ENST00000312457 57.90 78.14 70.32 0.57 0.42 0.43 1.53 0.73 0.90
ITPRIP ENST00000278071 57.91 80.02 71.47 0.57 0.37 0.46 1.53 0.61 0.86
FAM8A1 ENST00000259963 57.91 32.68 43.64 0.57 0.85 0.59 1.54 1.45 2.02
INTU ENST00000335251 57.92 38.48 46.90 0.56 0.73 0.70 1.54 1.69 1.88
PER1 ENST00000317276 57.92 24.81 39.72 0.56 1.33 0.78 1.53 1.05 2.02
CNDP2 ENST00000324262 57.93 53.12 55.13 0.56 0.67 0.51 1.53 1.77 1.74
C17orf67 ENST00000397861 57.93 94.58 79.53 0.56 0.23 0.38 1.53 0.24 0.52
SOD3 ENST00000382120 57.94 85.03 74.36 0.56 0.25 0.40 1.53 0.45 0.70
PIGM ENST00000368090 57.94 69.63 65.25 0.56 0.53 0.53 1.53 1.12 1.31
P2RY6 ENST00000393590 57.95 93.66 79.11 0.56 0.28 0.39 1.53 0.27 0.54
DNAAF2 ENST00000298292 57.95 58.49 58.29 0.56 0.54 0.48 1.53 1.39 1.65
C1QTNF2 ENST00000393975 57.96 66.81 63.58 0.56 0.54 0.49 1.53 1.23 1.41
ASB3 ENST00000406625 57.96 50.44 53.63 0.56 0.63 0.63 1.53 1.95 1.81
TSNAXIP1 ENST00000388833 57.97 79.32 71.08 0.56 0.38 0.43 1.53 0.67 0.86
TTI2 ENST00000431156 57.97 58.29 58.20 0.56 0.54 0.48 1.53 1.43 1.65
OR51J1 ENST00000332043 57.98 46.58 51.40 0.56 0.75 0.63 1.53 2.01 1.90

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