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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
UBE2C ENST00000356455 35.45 49.23 40.55 0.97 0.66 0.80 1.89 2.02 2.04
G6PC2 ENST00000375363 35.46 89.04 63.41 0.97 0.27 0.49 1.89 0.35 1.37
TMEM120B ENST00000449592 35.49 25.44 28.63 0.96 1.25 0.80 1.89 1.05 1.34
NOC3L ENST00000371361 35.50 46.52 39.37 0.96 0.73 0.80 1.89 2.02 2.04
OPRK1 ENST00000265572 35.50 72.90 53.62 0.96 0.49 0.63 1.89 1.03 1.82
MEGF9 ENST00000373930 35.51 11.00 21.37 0.96 2.09 1.34 1.89 0.52 0.91
PARL ENST00000317096 35.53 40.25 35.99 0.97 0.61 0.87 1.89 1.73 1.78
MATN2 ENST00000520016 35.54 46.06 39.17 0.97 0.76 0.78 1.89 2.03 2.06
SPARC ENST00000231061 35.55 18.68 25.19 0.97 1.52 1.05 1.89 0.75 1.17
SNX10 ENST00000338523 35.56 81.48 58.59 0.97 0.33 0.51 1.89 0.54 1.65
DEFB123 ENST00000376309 35.56 85.31 61.05 0.97 0.25 0.43 1.89 0.46 1.55
FAM73B ENST00000358369 35.57 27.59 29.74 0.97 1.25 0.86 1.89 1.17 1.42
KSR1 ENST00000398988 35.57 21.31 26.58 0.97 1.42 0.97 1.89 0.80 1.25
VKORC1 ENST00000394975 35.62 56.52 44.58 0.97 0.52 0.62 1.89 1.53 2.05
PTPRU ENST00000345512 35.62 15.04 23.43 0.97 1.91 1.19 1.89 0.64 1.01
GABRR1 ENST00000454853 35.63 67.62 50.69 0.97 0.53 0.66 1.89 1.19 1.85
NRG1 ENST00000356819 35.63 10.07 20.99 0.97 2.33 1.43 1.89 0.49 0.88
DMWD ENST00000270223 35.64 21.78 26.89 0.97 1.46 0.97 1.89 0.81 1.27
TP53BP2 ENST00000343537 35.64 19.30 25.57 0.97 1.46 1.05 1.89 0.75 1.19
COA1 ENST00000395879 35.65 69.76 51.86 0.97 0.53 0.62 1.89 1.13 1.92
AP5M1 ENST00000261558 35.79 59.19 46.18 0.95 0.49 0.67 1.89 1.44 1.95
IL1R1 ENST00000410023 35.80 25.83 28.97 0.95 1.21 0.81 1.89 1.07 1.31
CHKA ENST00000265689 35.46 24.10 27.93 0.97 1.37 0.85 1.90 0.98 1.29
CTXN3 ENST00000379445 35.49 87.87 62.57 0.96 0.24 0.48 1.90 0.38 1.40
RNF152 ENST00000312828 35.51 61.73 47.38 0.96 0.57 0.65 1.90 1.37 1.85

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