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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
SDR9C7 ENST00000293502 43.78 49.50 45.35 0.75 0.65 0.70 1.78 2.03 1.99
ST18 ENST00000276480 43.78 11.44 25.70 0.75 2.10 1.05 1.78 0.56 1.22
CAMK1 ENST00000256460 43.79 43.52 41.88 0.75 0.59 0.68 1.77 1.97 2.01
SCNM1 ENST00000368905 43.79 59.72 50.81 0.75 0.52 0.67 1.77 1.38 1.84
SLC25A53 ENST00000357421 43.80 56.14 48.87 0.75 0.52 0.71 1.77 1.55 1.85
FITM2 ENST00000396825 43.80 81.99 64.19 0.75 0.35 0.51 1.77 0.50 1.36
LIFR ENST00000263409 43.81 36.35 38.37 0.75 0.82 0.84 1.77 1.63 2.04
CXCR6 ENST00000458629 43.81 82.05 64.22 0.75 0.34 0.51 1.77 0.51 1.35
CCDC134 ENST00000255784 43.82 80.37 63.18 0.75 0.37 0.49 1.77 0.59 1.37
ANXA3 ENST00000264908 43.83 70.40 56.96 0.75 0.52 0.49 1.78 1.08 1.72
RREB1 ENST00000379938 43.83 3.29 21.70 0.75 3.44 1.25 1.78 0.27 0.92
THBS2 ENST00000366787 43.84 15.05 27.58 0.75 1.90 0.96 1.78 0.65 1.26
HAPLN1 ENST00000274341 43.84 24.07 32.16 0.75 1.37 0.91 1.78 0.97 1.59
CDH1 ENST00000261769 43.85 21.24 30.81 0.75 1.42 0.78 1.78 0.81 1.49
ZSCAN29 ENST00000396976 43.85 47.68 44.25 0.75 0.61 0.62 1.78 1.97 2.05
TNNT1 ENST00000588981 43.86 76.70 60.90 0.75 0.40 0.43 1.78 0.83 1.58
RIOK3 ENST00000339486 43.86 43.96 42.15 0.73 0.61 0.68 1.78 1.97 2.01
FMO1 ENST00000354841 43.87 58.40 50.15 0.73 0.54 0.63 1.78 1.41 1.90
EPS8 ENST00000281172 43.87 13.81 27.02 0.73 2.06 0.99 1.78 0.60 1.29
ALX3 ENST00000369792 43.88 68.76 56.02 0.73 0.53 0.49 1.78 1.18 1.77
LGI3 ENST00000306317 43.88 41.13 40.66 0.73 0.59 0.81 1.78 1.82 2.05
TTC33 ENST00000337702 43.89 57.99 49.92 0.73 0.54 0.62 1.78 1.44 1.89
CD274 ENST00000381577 43.89 41.83 41.07 0.73 0.59 0.75 1.77 1.80 2.05
POLR1E ENST00000377798 43.90 46.85 43.73 0.73 0.71 0.61 1.78 1.97 2.02
PTS ENST00000280362 43.90 86.36 66.85 0.73 0.25 0.53 1.78 0.42 1.20

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