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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
BUD31 ENST00000403633 13.43 47.00 28.42 1.67 0.70 0.78 0.67 1.97 1.29
KIAA1429 ENST00000297591 13.44 9.50 8.83 1.67 2.48 2.49 0.67 0.49 0.38
HBEGF ENST00000230990 13.44 50.89 30.34 1.67 0.63 0.82 0.67 1.92 1.45
NRN1 ENST00000244766 13.45 22.68 15.91 1.67 1.46 1.76 0.67 0.88 0.66
FERMT2 ENST00000343279 13.45 2.27 5.12 1.66 3.64 3.61 0.67 0.30 0.25
KCNK10 ENST00000319231 13.46 35.48 22.63 1.66 0.77 1.16 0.67 1.56 0.96
IQGAP1 ENST00000268182 13.47 10.67 9.52 1.66 2.14 2.30 0.68 0.51 0.40
SENP5 ENST00000323460 13.47 5.09 6.67 1.66 3.20 3.00 0.68 0.33 0.32
RPL31 ENST00000409028 13.48 23.36 16.22 1.66 1.42 1.71 0.68 0.93 0.65
HDAC4 ENST00000345617 13.48 0.13 4.10 1.66 4.12 3.76 0.68 0.28 0.23
ZBTB6 ENST00000373659 13.49 32.43 21.08 1.64 0.87 1.42 0.68 1.48 0.89
PRDM1 ENST00000369096 13.49 11.12 9.85 1.64 2.09 2.30 0.68 0.53 0.40
PRDM14 ENST00000276594 13.50 30.46 20.04 1.64 1.09 1.49 0.68 1.39 0.85
CNP ENST00000393892 13.50 12.79 10.74 1.64 2.07 2.19 0.68 0.59 0.43
NPR2 ENST00000342694 13.51 23.99 16.57 1.64 1.37 1.71 0.68 0.95 0.71
USP39 ENST00000323701 13.51 28.61 19.05 1.64 1.16 1.54 0.68 1.29 0.85
ATG3 ENST00000283290 13.52 34.22 21.99 1.64 0.84 1.19 0.68 1.56 0.97
SLC6A11 ENST00000254488 13.52 31.34 20.57 1.64 0.97 1.48 0.68 1.40 0.89
ILKAP ENST00000254654 13.53 11.99 10.29 1.63 2.07 2.19 0.68 0.58 0.42
MAN1A1 ENST00000368468 13.53 22.67 15.93 1.64 1.46 1.76 0.68 0.88 0.66
TAF5L ENST00000258281 13.54 5.41 6.80 1.64 3.06 2.97 0.68 0.33 0.32
KCNQ4 ENST00000347132 13.54 16.75 12.69 1.64 1.68 2.18 0.68 0.71 0.52
ADARB1 ENST00000539173 13.55 11.97 10.32 1.64 2.07 2.19 0.68 0.59 0.43
SYT2 ENST00000367267 13.55 10.99 9.77 1.64 2.09 2.29 0.68 0.52 0.40
ATP13A3 ENST00000439040 13.56 6.86 7.57 1.64 2.62 2.75 0.68 0.37 0.33

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