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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
CAGE1 ENST00000502583 76.32 49.59 64.24 0.34 0.66 0.51 0.74 2.02 1.35
CRIP1 ENST00000330233 76.32 88.06 85.53 0.34 0.24 0.33 0.74 0.38 0.35
LTB4R2 ENST00000528054 76.33 76.82 79.89 0.34 0.42 0.37 0.74 0.81 0.52
SERPINA10 ENST00000393096 76.33 85.86 84.43 0.34 0.28 0.33 0.74 0.43 0.40
C16orf54 ENST00000329410 76.34 61.82 71.63 0.34 0.57 0.44 0.74 1.37 0.83
GPC1 ENST00000264039 76.34 31.85 53.50 0.34 0.94 0.63 0.74 1.48 1.82
PHF11 ENST00000378319 76.35 71.84 77.25 0.34 0.51 0.35 0.74 1.07 0.58
EID2 ENST00000390658 76.35 66.33 74.20 0.34 0.54 0.39 0.74 1.20 0.69
BAALC ENST00000309982 76.36 81.00 82.05 0.33 0.35 0.35 0.74 0.55 0.46
ZADH2 ENST00000322342 76.36 69.62 76.00 0.33 0.53 0.38 0.74 1.11 0.62
PLVAP ENST00000252590 76.37 52.77 66.24 0.33 0.66 0.52 0.74 1.80 1.20
ZNF541 ENST00000314121 76.38 3.54 38.25 0.33 3.38 0.85 0.74 0.30 2.04
TAS2R41 ENST00000408916 76.38 95.40 89.01 0.33 0.24 0.19 0.74 0.21 0.27
FN3K ENST00000300784 76.39 74.25 78.59 0.33 0.53 0.38 0.74 1.02 0.54
ZNF33A ENST00000374618 76.39 50.04 64.54 0.33 0.66 0.51 0.74 2.01 1.34
DPH3 ENST00000488423 76.40 80.03 81.59 0.33 0.37 0.35 0.74 0.60 0.47
CTSV ENST00000259470 76.40 69.12 75.77 0.33 0.56 0.38 0.73 1.13 0.64
TMEM126B ENST00000358867 76.41 80.39 81.77 0.33 0.37 0.37 0.73 0.59 0.47
KRTAP5-6 ENST00000382160 76.41 91.75 87.24 0.33 0.24 0.28 0.73 0.32 0.31
MAP3K15 ENST00000338883 76.42 71.80 77.26 0.33 0.51 0.35 0.73 1.07 0.58
TSPEAR ENST00000323084 76.42 64.30 73.10 0.33 0.49 0.42 0.73 1.20 0.80
SAPCD2 ENST00000409687 76.43 48.58 63.74 0.33 0.65 0.49 0.73 2.01 1.38
LRRC14B ENST00000328278 76.43 86.01 84.57 0.33 0.25 0.34 0.73 0.43 0.40
C22orf15 ENST00000402217 76.44 68.72 75.53 0.33 0.53 0.37 0.73 1.17 0.66
GJC3 ENST00000312891 76.44 73.80 78.37 0.33 0.53 0.38 0.73 1.02 0.54

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