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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
SLC38A2 ENST00000256689 23.38 8.39 13.51 1.38 2.53 2.05 1.08 0.46 0.57
ERCC6L ENST00000334463 23.38 6.43 12.47 1.38 2.63 2.23 1.08 0.37 0.50
ROMO1 ENST00000374078 23.39 74.96 48.04 1.37 0.53 0.67 1.08 0.93 1.88
PTPRO ENST00000281171 23.39 22.98 21.27 1.37 1.46 1.39 1.09 0.90 0.90
ARHGAP25 ENST00000409202 23.40 15.86 17.46 1.37 1.89 1.62 1.10 0.68 0.75
PTGDR2 ENST00000332539 23.40 85.91 54.16 1.37 0.28 0.61 1.10 0.43 1.74
SECISBP2L ENST00000559471 23.41 14.01 16.54 1.37 2.06 1.71 1.10 0.59 0.70
USP2 ENST00000260187 23.41 29.33 24.42 1.37 1.13 1.08 1.10 1.36 1.08
GOT2 ENST00000245206 23.42 32.48 26.12 1.37 0.86 0.99 1.10 1.48 1.27
FLNC ENST00000325888 23.42 9.51 14.19 1.37 2.51 1.99 1.10 0.49 0.60
CSNK1G2 ENST00000255641 23.43 9.37 14.11 1.37 2.48 2.02 1.10 0.49 0.60
TTC18 ENST00000310715 23.43 27.63 23.63 1.37 1.27 1.19 1.10 1.17 1.01
CDK9 ENST00000373264 23.44 50.94 35.40 1.37 0.65 0.87 1.10 1.94 1.76
TMEM110-MUSTN1 ENST00000504329 23.44 37.30 28.54 1.37 0.76 0.78 1.09 1.66 1.33
ZNF346 ENST00000358149 23.45 36.16 27.98 1.37 0.82 0.82 1.09 1.60 1.27
FAM135A ENST00000418814 23.45 10.31 14.63 1.37 2.26 1.97 1.09 0.49 0.59
ARID1B ENST00000346085 23.46 1.25 9.89 1.37 3.99 2.30 1.09 0.27 0.41
PITPNM3 ENST00000262483 23.46 5.91 12.26 1.37 2.82 2.25 1.09 0.35 0.50
PPM1B ENST00000282412 23.47 37.77 28.75 1.38 0.80 0.80 1.08 1.70 1.32
PHEX ENST00000379374 23.48 2.64 10.65 1.38 3.54 2.18 1.08 0.29 0.43
TFCP2L1 ENST00000263707 23.48 2.91 10.81 1.38 3.49 2.19 1.08 0.29 0.43
DLG1 ENST00000346964 23.49 11.80 15.46 1.38 2.09 1.81 1.08 0.57 0.67
SMG5 ENST00000361813 23.49 19.51 19.49 1.38 1.44 1.54 1.08 0.74 0.84
HOXA3 ENST00000396352 23.50 15.94 17.58 1.38 1.87 1.63 1.08 0.68 0.77
KCNH8 ENST00000328405 23.50 34.80 27.28 1.38 0.77 0.97 1.08 1.55 1.25

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