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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
GTF3C2 ENST00000359541 9.43 11.64 7.88 2.19 2.09 2.62 0.47 0.57 0.35
SMAD1 ENST00000515385 9.44 10.09 7.14 2.19 2.33 2.87 0.47 0.49 0.33
TTLL7 ENST00000260505 9.44 19.12 11.87 2.19 1.49 2.24 0.47 0.76 0.46
CA10 ENST00000451037 9.45 23.28 14.07 2.19 1.43 2.04 0.47 0.93 0.60
FST ENST00000256759 9.45 11.57 7.87 2.19 2.10 2.63 0.46 0.57 0.35
AKT2 ENST00000392038 9.46 20.35 12.46 2.19 1.44 2.23 0.46 0.75 0.50
TMEM203 ENST00000343666 9.46 48.20 27.01 2.20 0.63 1.00 0.45 1.99 1.29
DGCR8 ENST00000351989 9.47 6.58 5.29 2.19 2.63 3.56 0.45 0.37 0.25
RPS21 ENST00000343986 9.47 57.99 31.94 2.19 0.56 0.91 0.45 1.44 1.57
LHX1 ENST00000254457 9.48 27.93 16.53 2.18 1.20 1.71 0.45 1.19 0.69
INPP5D ENST00000359570 9.48 13.15 8.66 2.18 2.06 2.52 0.45 0.60 0.36
LPCAT3 ENST00000261407 9.49 11.76 8.00 2.16 2.09 2.59 0.45 0.57 0.37
MAP3K7 ENST00000369329 9.49 4.17 4.12 2.16 3.26 3.77 0.46 0.32 0.24
COPA ENST00000368069 9.50 0.73 2.61 2.16 4.09 4.01 0.46 0.28 0.23
EIF3I ENST00000373586 9.50 15.53 10.08 2.16 1.87 2.26 0.46 0.67 0.42
NOSIP ENST00000391853 9.51 58.85 32.38 2.16 0.54 0.91 0.46 1.41 1.61
RNF20 ENST00000389120 9.51 31.90 18.71 2.16 0.94 1.57 0.47 1.48 0.81
ENAH ENST00000366844 9.52 4.96 4.56 2.16 3.25 3.71 0.47 0.32 0.25
RAB8B ENST00000321437 9.52 54.28 30.10 2.15 0.62 0.81 0.47 1.69 1.46
GPR85 ENST00000297146 9.53 25.63 15.35 2.15 1.24 1.80 0.47 1.05 0.66
UNC13A ENST00000519716 9.53 3.38 3.82 2.16 3.43 3.77 0.47 0.29 0.24
RPL37A ENST00000491306 9.54 77.96 41.97 2.16 0.42 0.68 0.47 0.79 2.00
ZFP62 ENST00000502412 9.54 20.45 12.55 2.16 1.43 2.21 0.47 0.76 0.51
HDAC1 ENST00000373548 9.55 19.78 12.23 2.16 1.42 2.26 0.47 0.74 0.50
DNM2 ENST00000389253 9.56 4.75 4.43 2.16 3.27 3.72 0.47 0.32 0.25

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