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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
NDUFA13 ENST00000507754 59.92 87.20 76.66 0.63 0.20 0.37 1.39 0.41 0.61
SIPA1 ENST00000394224 59.92 24.95 40.63 0.63 1.32 0.81 1.39 1.07 2.05
ZNF804A ENST00000302277 59.93 21.40 39.00 0.63 1.43 0.80 1.39 0.80 2.06
ANKRD7 ENST00000265224 59.93 71.94 67.85 0.62 0.51 0.51 1.39 1.06 1.11
SNX19 ENST00000265909 59.94 48.07 53.43 0.62 0.63 0.62 1.39 1.99 1.83
CATSPER4 ENST00000456354 59.95 66.24 64.36 0.62 0.53 0.51 1.39 1.20 1.34
FGGY ENST00000371218 59.95 67.50 65.18 0.62 0.54 0.52 1.39 1.20 1.30
CYP4B1 ENST00000371923 59.96 60.71 60.96 0.62 0.56 0.43 1.40 1.39 1.58
PTRHD1 ENST00000328379 59.96 96.65 81.71 0.62 0.23 0.35 1.40 0.20 0.47
MRPL50 ENST00000374865 59.97 85.42 75.68 0.62 0.25 0.38 1.40 0.45 0.64
C21orf62 ENST00000536776 59.97 86.19 76.12 0.62 0.27 0.38 1.40 0.42 0.62
ZNF692 ENST00000451251 59.98 64.85 63.63 0.62 0.48 0.49 1.40 1.24 1.39
TMPRSS3 ENST00000291532 59.98 62.20 61.79 0.62 0.52 0.46 1.39 1.35 1.46
TXNRD2 ENST00000400521 59.99 57.04 58.60 0.62 0.56 0.51 1.40 1.52 1.65
NYAP1 ENST00000300179 59.99 5.59 31.00 0.62 2.99 0.82 1.40 0.33 1.52
ROPN1 ENST00000184183 60.00 69.91 66.66 0.62 0.53 0.53 1.40 1.15 1.20
SGSH ENST00000326317 60.00 41.86 49.90 0.63 0.61 0.63 1.40 1.80 1.89
RNASE7 ENST00000298690 60.01 90.43 78.45 0.63 0.25 0.38 1.40 0.37 0.54
ASPM ENST00000367409 60.01 38.29 48.00 0.63 0.75 0.67 1.40 1.72 1.87
BPHL ENST00000380379 60.02 74.10 69.15 0.63 0.53 0.44 1.40 1.03 0.99
TTC12 ENST00000529221 60.02 58.52 59.59 0.63 0.54 0.49 1.39 1.40 1.69
ZNF335 ENST00000322927 60.03 26.19 41.33 0.63 1.19 0.73 1.39 1.08 2.01
AC093157.1 ENST00000593496 60.03 87.51 76.92 0.63 0.23 0.35 1.39 0.38 0.60
TSPYL2 ENST00000375442 60.04 18.42 37.48 0.63 1.47 0.85 1.39 0.75 2.01
WDR5B ENST00000330689 60.04 77.07 70.92 0.63 0.42 0.43 1.39 0.78 0.86

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