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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
DDX11 ENST00000407793 71.54 50.74 61.91 0.38 0.63 0.48 0.82 1.94 1.45
MESDC2 ENST00000261758 71.55 33.16 51.50 0.38 0.82 0.63 0.82 1.51 1.92
CLDN25 ENST00000453129 71.55 96.18 87.06 0.38 0.22 0.28 0.82 0.20 0.30
F8A1 ENST00000369446 71.56 99.59 88.75 0.38 0.16 0.20 0.82 0.12 0.28
SPDYC ENST00000377185 71.56 58.72 66.86 0.38 0.54 0.53 0.82 1.43 1.20
KRT9 ENST00000246662 71.57 50.45 61.73 0.38 0.65 0.46 0.82 1.95 1.46
GOLM1 ENST00000388712 71.57 55.59 65.02 0.38 0.53 0.51 0.82 1.59 1.31
OR8B12 ENST00000306842 71.58 70.48 73.80 0.38 0.52 0.42 0.82 1.08 0.71
CLIC6 ENST00000349499 71.58 62.43 69.10 0.38 0.52 0.44 0.82 1.32 1.00
SLC25A47 ENST00000361529 71.59 84.94 81.65 0.38 0.27 0.37 0.82 0.45 0.47
SIRPB2 ENST00000359801 71.59 63.90 69.99 0.38 0.48 0.47 0.82 1.22 0.92
C10orf88 ENST00000481909 71.60 37.81 54.24 0.38 0.80 0.59 0.82 1.69 1.74
PNLIPRP3 ENST00000369230 71.60 67.83 72.39 0.38 0.52 0.44 0.82 1.17 0.83
GBE1 ENST00000429644 71.61 53.27 63.65 0.38 0.66 0.49 0.82 1.73 1.38
AVP ENST00000380293 71.61 78.04 78.02 0.38 0.42 0.38 0.82 0.76 0.54
PIGR ENST00000356495 71.62 16.92 42.52 0.38 1.66 0.68 0.82 0.71 2.01
PLA2G7 ENST00000274793 71.62 85.34 81.84 0.38 0.25 0.37 0.82 0.45 0.47
FMN1 ENST00000334528 71.63 47.76 60.11 0.38 0.59 0.48 0.82 1.99 1.61
SLC22A1 ENST00000366963 71.63 84.68 81.52 0.38 0.27 0.35 0.82 0.42 0.48
BMP8B ENST00000372827 71.64 72.66 75.08 0.38 0.47 0.39 0.82 1.04 0.67
HPDL ENST00000334815 71.64 77.81 77.92 0.37 0.42 0.38 0.82 0.79 0.54
ALPK1 ENST00000458497 71.65 51.38 62.36 0.37 0.63 0.48 0.82 1.89 1.41
NPM3 ENST00000370110 71.65 56.35 65.56 0.37 0.52 0.52 0.82 1.53 1.30
COL6A5 ENST00000265379 71.66 50.74 61.95 0.37 0.63 0.48 0.82 1.94 1.46
PARK2 ENST00000366898 71.66 46.11 59.00 0.37 0.75 0.48 0.82 2.03 1.65

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