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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
C1orf52 ENST00000471115 63.15 59.64 62.22 0.59 0.52 0.48 1.26 1.40 1.44
SLC9B2 ENST00000394785 63.15 45.08 53.51 0.59 0.67 0.63 1.26 1.97 1.82
LYZ ENST00000261267 63.16 88.83 79.30 0.59 0.25 0.39 1.26 0.35 0.53
RGS21 ENST00000417209 63.16 84.74 77.11 0.59 0.27 0.37 1.26 0.42 0.60
TMEM234 ENST00000309777 63.17 89.56 79.62 0.59 0.27 0.38 1.26 0.36 0.53
CTNS ENST00000381870 63.17 40.42 50.89 0.59 0.61 0.67 1.26 1.76 1.85
TCF25 ENST00000263346 63.18 18.43 39.19 0.59 1.48 0.78 1.26 0.75 2.06
CCDC28B ENST00000373602 63.18 95.66 82.82 0.59 0.23 0.32 1.25 0.20 0.42
TTC7A ENST00000319190 63.19 71.74 69.69 0.59 0.51 0.44 1.25 1.07 0.95
AMTN ENST00000339336 63.19 90.47 80.17 0.59 0.25 0.35 1.25 0.37 0.53
AGRP ENST00000290953 63.20 85.75 77.68 0.59 0.27 0.38 1.25 0.44 0.55
NDUFB11 ENST00000276062 63.20 27.57 43.75 0.59 1.25 0.61 1.25 1.17 2.02
NYX ENST00000342595 63.21 63.40 64.66 0.59 0.48 0.51 1.26 1.28 1.32
GAS2L3 ENST00000539410 63.21 60.60 62.91 0.59 0.53 0.51 1.26 1.41 1.40
RPL3L ENST00000268661 63.22 82.26 75.73 0.59 0.34 0.38 1.26 0.52 0.64
CAPSL ENST00000397367 63.23 81.94 75.54 0.59 0.35 0.37 1.26 0.51 0.65
OR6Q1 ENST00000302622 63.23 75.11 71.72 0.59 0.51 0.46 1.26 0.91 0.82
ZNF180 ENST00000221327 63.24 42.38 52.05 0.59 0.59 0.62 1.26 1.90 1.94
DYX1C1 ENST00000321149 63.24 62.54 64.17 0.59 0.53 0.51 1.26 1.31 1.37
MPLKIP ENST00000306984 63.25 83.09 76.24 0.59 0.29 0.37 1.25 0.49 0.61
STAB2 ENST00000388887 63.25 46.66 54.52 0.59 0.75 0.57 1.25 1.97 1.75
SAMD3 ENST00000368134 63.26 67.27 67.01 0.59 0.56 0.52 1.25 1.21 1.19
F11 ENST00000403665 63.26 76.87 72.79 0.59 0.43 0.43 1.25 0.81 0.81
TBCE ENST00000366601 63.27 43.40 52.66 0.59 0.61 0.59 1.25 1.95 1.89
MTFR2 ENST00000420702 63.27 60.99 63.26 0.59 0.54 0.49 1.25 1.41 1.36

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