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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
AXL ENST00000301178 41.20 20.56 29.03 0.85 1.44 0.82 1.70 0.76 1.31
DSCC1 ENST00000313655 41.20 36.17 36.89 0.85 0.82 0.81 1.70 1.60 1.94
SV2C ENST00000502798 41.21 32.55 35.06 0.85 0.86 0.86 1.70 1.49 1.75
ABHD12 ENST00000376542 41.21 41.17 39.53 0.85 0.59 0.80 1.71 1.82 2.03
RFX5 ENST00000290524 41.22 60.61 49.89 0.84 0.53 0.63 1.71 1.41 1.89
RHOJ ENST00000316754 41.22 54.60 46.57 0.84 0.59 0.66 1.71 1.66 1.89
SLMO1 ENST00000440960 41.23 92.85 69.12 0.84 0.29 0.44 1.71 0.30 1.00
TMEM53 ENST00000372237 41.23 61.10 50.19 0.84 0.53 0.63 1.70 1.39 1.90
METAP1 ENST00000296411 41.24 26.11 31.88 0.84 1.20 0.91 1.70 1.09 1.58
DUT ENST00000331200 41.24 61.62 50.45 0.84 0.54 0.67 1.70 1.40 1.88
LRIF1 ENST00000369763 41.25 35.09 36.28 0.84 0.76 0.85 1.70 1.57 1.85
GRAMD1A ENST00000317991 41.25 26.33 31.99 0.84 1.19 0.90 1.70 1.08 1.59
CEBPE ENST00000206513 41.26 54.08 46.34 0.84 0.65 0.67 1.69 1.68 1.90
ANKRD1 ENST00000371697 41.26 71.85 56.35 0.84 0.51 0.49 1.69 1.07 1.75
HIST1H2AI ENST00000358739 41.27 90.94 68.07 0.84 0.25 0.51 1.69 0.35 1.10
MAPK1IP1L ENST00000395468 41.27 31.62 34.67 0.84 0.95 0.90 1.69 1.44 1.76
CHSY3 ENST00000305031 41.28 28.46 33.00 0.84 1.15 0.85 1.69 1.24 1.67
HRH1 ENST00000397056 41.28 68.92 54.73 0.84 0.54 0.56 1.68 1.17 1.73
IL13RA1 ENST00000371666 41.29 13.99 25.75 0.84 2.06 1.04 1.68 0.60 1.22
KCTD8 ENST00000360029 41.29 62.23 50.83 0.84 0.53 0.67 1.68 1.33 1.85
S100G ENST00000380200 41.30 90.85 67.99 0.84 0.25 0.51 1.68 0.35 1.10
CLDN1 ENST00000295522 41.30 63.26 51.39 0.84 0.47 0.63 1.68 1.31 1.90
NBN ENST00000265433 41.31 55.36 47.08 0.84 0.58 0.68 1.68 1.61 1.88
SYNPO2 ENST00000307142 41.32 30.55 34.11 0.84 1.08 0.90 1.68 1.38 1.75
CPNE2 ENST00000535318 41.32 28.72 33.17 0.84 1.15 0.87 1.68 1.29 1.69

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