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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
FBXL19 ENST00000380310 46.75 1.20 22.06 0.56 4.02 1.15 1.82 0.27 0.96
ZNF112 ENST00000337401 46.75 25.35 34.34 0.56 1.28 0.87 1.82 1.03 1.77
RNF182 ENST00000488300 46.76 81.22 65.54 0.56 0.34 0.52 1.81 0.55 1.29
FTSJ3 ENST00000427159 46.76 19.05 31.10 0.56 1.52 0.84 1.81 0.76 1.51
PIGK ENST00000370812 46.77 40.92 42.07 0.56 0.61 0.71 1.81 1.78 1.99
TPGS2 ENST00000334295 46.77 56.81 50.91 0.56 0.54 0.66 1.81 1.54 1.85
FOSL1 ENST00000312562 46.78 38.70 40.95 0.56 0.70 0.77 1.81 1.67 2.05
NDUFS8 ENST00000313468 46.78 52.45 48.48 0.56 0.65 0.68 1.81 1.84 1.86
CA12 ENST00000178638 46.79 71.17 59.16 0.56 0.52 0.49 1.80 1.06 1.68
L3MBTL1 ENST00000427442 46.80 40.20 41.72 0.56 0.61 0.72 1.80 1.72 2.01
WNT1 ENST00000293549 46.80 34.07 38.69 0.56 0.82 0.82 1.80 1.54 2.02
RFC4 ENST00000392481 46.81 48.49 46.33 0.56 0.65 0.67 1.80 2.02 1.90
MAP3K19 ENST00000375845 46.81 55.91 50.41 0.56 0.51 0.67 1.81 1.56 1.90
DHX32 ENST00000284690 46.82 45.88 44.99 0.56 0.75 0.68 1.81 2.02 2.04
MS4A1 ENST00000534668 46.82 73.53 60.76 0.56 0.53 0.44 1.81 1.03 1.61
UTP23 ENST00000309822 46.83 49.16 46.66 0.56 0.66 0.66 1.81 2.04 1.87
LMO7 ENST00000465261 46.83 19.67 31.48 0.56 1.43 0.86 1.82 0.74 1.57
SCARA5 ENST00000354914 46.84 46.56 45.42 0.56 0.75 0.70 1.82 2.01 2.00
C3orf18 ENST00000357203 46.84 86.28 68.55 0.56 0.25 0.47 1.82 0.42 1.05
DSG1 ENST00000257192 46.85 14.97 29.06 0.56 1.92 0.82 1.82 0.64 1.32
PIH1D1 ENST00000262265 46.85 53.52 49.11 0.56 0.65 0.72 1.82 1.70 1.83
TMPRSS15 ENST00000284885 46.86 61.29 53.47 0.56 0.54 0.63 1.82 1.39 1.82
OS9 ENST00000315970 46.86 40.35 41.82 0.56 0.61 0.71 1.82 1.75 2.02
CCDC147 ENST00000369704 46.87 55.73 50.34 0.56 0.52 0.66 1.82 1.59 1.92
ITGB2 ENST00000397850 46.87 53.39 49.01 0.56 0.65 0.72 1.82 1.70 1.84

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