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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
MICAL2 ENST00000256194 33.58 34.99 32.48 0.95 0.75 0.89 1.70 1.56 1.63
GNRHR ENST00000226413 33.58 39.97 34.96 0.95 0.63 0.90 1.70 1.68 1.74
PTDSS2 ENST00000308020 33.59 37.73 33.81 0.95 0.80 0.89 1.70 1.70 1.73
KLRG1 ENST00000356986 33.59 66.53 48.95 0.95 0.57 0.71 1.70 1.21 1.84
ZNF668 ENST00000539836 33.60 25.97 27.95 0.96 1.20 0.82 1.70 1.10 1.28
TTC9 ENST00000256367 33.60 55.55 42.89 0.96 0.54 0.67 1.71 1.60 1.99
MCM3 ENST00000596288 33.61 40.94 35.47 0.96 0.61 0.87 1.71 1.79 1.77
MMS22L ENST00000275053 33.61 19.94 24.82 0.96 1.47 1.04 1.71 0.73 1.10
NDNF ENST00000379692 33.62 25.13 27.50 0.96 1.32 0.97 1.72 1.03 1.27
SULF2 ENST00000359930 33.62 21.78 25.84 0.96 1.46 1.01 1.72 0.81 1.23
MKNK1 ENST00000371946 33.63 56.42 43.38 0.96 0.52 0.63 1.71 1.53 2.00
IFT172 ENST00000260570 33.63 38.53 34.36 0.96 0.73 0.87 1.71 1.67 1.77
HIPK4 ENST00000291823 33.64 47.30 38.74 0.96 0.67 0.82 1.72 2.00 2.02
YLPM1 ENST00000325680 33.64 7.86 18.77 0.96 2.54 1.57 1.72 0.44 0.82
CRTC2 ENST00000368633 33.65 9.02 19.36 0.96 2.43 1.54 1.71 0.47 0.85
VEZT ENST00000436874 33.66 19.66 24.72 0.96 1.43 1.05 1.71 0.74 1.10
PPP1R1B ENST00000254079 33.66 34.19 32.11 0.96 0.84 0.90 1.71 1.55 1.60
CLCN2 ENST00000265593 33.67 41.78 35.82 0.96 0.61 0.86 1.71 1.78 1.79
PDCD4 ENST00000280154 33.67 51.14 40.58 0.96 0.66 0.81 1.70 1.91 2.04
DTX1 ENST00000257600 33.68 32.78 31.45 0.96 0.84 0.87 1.70 1.44 1.56
ACP2 ENST00000256997 33.68 35.02 32.53 0.96 0.75 0.89 1.70 1.58 1.61
LIX1 ENST00000274382 33.69 46.69 38.46 0.96 0.73 0.84 1.70 1.97 2.04
DSEL ENST00000310045 33.69 30.56 30.32 0.95 1.08 0.84 1.70 1.39 1.45
ADAT2 ENST00000237283 33.70 81.01 57.23 0.95 0.35 0.52 1.70 0.55 1.69
AMIGO2 ENST00000266581 33.70 28.14 29.07 0.94 1.18 0.84 1.70 1.20 1.32

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