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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
PHLDB3 ENST00000292140 80.45 68.15 77.53 0.33 0.52 0.35 0.59 1.22 0.57
MRPL55 ENST00000366731 80.46 61.58 73.81 0.33 0.54 0.42 0.59 1.41 0.71
CTSZ ENST00000217131 80.46 94.91 90.75 0.33 0.23 0.15 0.59 0.23 0.20
FGF19 ENST00000294312 80.47 63.51 74.91 0.33 0.49 0.39 0.59 1.25 0.64
SFI1 ENST00000400288 80.47 54.96 69.95 0.33 0.57 0.47 0.59 1.63 0.92
HIST1H4G ENST00000244537 80.48 96.34 91.32 0.33 0.22 0.15 0.58 0.19 0.18
ZFP57 ENST00000488757 80.48 74.60 80.87 0.33 0.53 0.39 0.58 0.99 0.51
TMEM257 ENST00000408967 80.49 92.74 89.72 0.33 0.29 0.18 0.58 0.30 0.23
MMP8 ENST00000236826 80.49 88.32 87.54 0.33 0.23 0.27 0.58 0.37 0.30
C1orf53 ENST00000367393 80.50 92.30 89.53 0.33 0.25 0.18 0.58 0.30 0.23
KIAA1755 ENST00000279024 80.50 56.06 70.59 0.33 0.49 0.43 0.58 1.55 0.90
MOB3A ENST00000357066 80.51 85.19 86.08 0.33 0.25 0.33 0.59 0.45 0.33
SRRM3 ENST00000326382 80.51 27.47 53.40 0.33 1.25 0.62 0.59 1.16 1.84
PARP10 ENST00000313028 80.52 39.50 60.53 0.33 0.70 0.44 0.59 1.63 1.58
TTC6 ENST00000553443 80.52 46.20 64.74 0.33 0.73 0.49 0.59 2.04 1.33
ALMS1 ENST00000264448 80.53 45.68 64.38 0.33 0.75 0.51 0.59 2.01 1.34
LCE3A ENST00000335674 80.53 98.16 92.35 0.33 0.20 0.14 0.59 0.16 0.15
LAMP3 ENST00000265598 80.54 52.78 68.67 0.33 0.66 0.47 0.58 1.80 1.05
RNASE12 ENST00000556526 80.54 89.42 88.12 0.33 0.27 0.23 0.58 0.37 0.30
CXorf40A ENST00000441248 80.55 58.19 71.96 0.33 0.54 0.43 0.58 1.44 0.80
SPON2 ENST00000290902 80.55 91.70 89.23 0.33 0.24 0.19 0.58 0.32 0.25
FDCSP ENST00000317987 80.56 77.88 82.63 0.33 0.42 0.32 0.58 0.79 0.43
C1orf56 ENST00000368926 80.56 83.78 85.51 0.33 0.27 0.33 0.58 0.47 0.35
THBD ENST00000377103 80.57 35.33 57.98 0.33 0.77 0.47 0.58 1.57 1.68
OR5W2 ENST00000344514 80.57 87.04 87.01 0.32 0.22 0.28 0.58 0.40 0.30

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