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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
WFDC9 ENST00000326000 98.90 88.96 96.69 0.10 0.25 0.08 0.11 0.35 0.08
AC138647.1 ENST00000427937 91.49 95.90 96.69 0.15 0.22 0.08 0.20 0.20 0.08
SPINT3 ENST00000217428 93.78 95.65 96.70 0.11 0.23 0.08 0.13 0.20 0.08
LY6D ENST00000301263 94.71 93.15 96.70 0.10 0.28 0.08 0.11 0.30 0.08
C12orf74 ENST00000397833 94.78 93.06 96.71 0.10 0.28 0.08 0.11 0.30 0.08
PRLH ENST00000165524 94.80 93.04 96.72 0.10 0.28 0.08 0.11 0.30 0.08
AP001885.1 ENST00000444002 93.36 99.53 96.72 0.15 0.16 0.08 0.15 0.13 0.08
C10orf105 ENST00000441508 93.16 94.46 96.73 0.15 0.23 0.08 0.16 0.24 0.08
ZNF776 ENST00000317178 96.49 91.38 96.73 0.10 0.23 0.08 0.11 0.33 0.08
RP11-481A20.11 ENST00000527396 90.43 96.10 96.74 0.15 0.21 0.08 0.25 0.20 0.08
CFHR5 ENST00000256785 96.89 91.04 96.74 0.09 0.25 0.08 0.11 0.36 0.08
ZNF616 ENST00000600228 97.60 90.31 96.75 0.10 0.25 0.08 0.11 0.38 0.08
C19orf24 ENST00000409293 91.22 96.21 96.75 0.15 0.22 0.08 0.21 0.20 0.08
NPIPB15 ENST00000429990 94.56 93.37 96.76 0.10 0.28 0.08 0.12 0.28 0.08
C9orf66 ENST00000382387 94.61 93.31 96.76 0.10 0.28 0.08 0.12 0.29 0.08
KRTAP19-4 ENST00000334058 88.23 98.09 96.77 0.22 0.20 0.08 0.34 0.16 0.08
RP11-763F8.1 ENST00000502368 94.09 94.48 96.77 0.11 0.23 0.08 0.13 0.24 0.08
PRAMEF14 ENST00000334600 94.34 93.57 96.78 0.10 0.28 0.08 0.11 0.28 0.08
LCE6A ENST00000431011 89.97 97.73 96.78 0.18 0.21 0.08 0.27 0.17 0.08
STATH ENST00000246895 98.43 89.50 96.79 0.10 0.27 0.08 0.11 0.36 0.08
ANKRD20A3 ENST00000254835 91.37 96.13 96.79 0.15 0.21 0.08 0.20 0.20 0.08
DUX4L4 ENST00000538692 90.81 98.14 96.80 0.16 0.20 0.08 0.21 0.16 0.07
RPS4Y2 ENST00000288666 90.53 95.61 96.80 0.16 0.23 0.08 0.24 0.21 0.07
PROL1 ENST00000399575 99.29 88.72 96.81 0.11 0.27 0.08 0.12 0.35 0.07
HRASLS2 ENST00000255695 97.28 90.74 96.81 0.10 0.25 0.08 0.11 0.35 0.07

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