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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
PRSS22 ENST00000161006 49.20 52.68 49.91 0.57 0.67 0.62 1.80 1.80 1.89
PTPN3 ENST00000374541 49.21 30.16 37.96 0.57 1.10 0.85 1.80 1.40 2.02
ZNF365 ENST00000410046 49.21 40.21 43.09 0.57 0.61 0.65 1.80 1.72 2.01
SSSCA1 ENST00000309328 49.22 86.97 70.40 0.57 0.22 0.43 1.80 0.40 0.91
ELP6 ENST00000296149 49.22 58.34 53.24 0.57 0.54 0.61 1.80 1.41 1.88
HSF1 ENST00000528838 49.23 15.33 30.48 0.57 1.89 0.80 1.80 0.67 1.46
ZXDB ENST00000374888 49.23 13.92 29.75 0.57 2.04 0.86 1.80 0.60 1.42
HLA-DQA1 ENST00000343139 49.24 51.28 49.18 0.57 0.65 0.72 1.80 1.90 1.84
HS3ST1 ENST00000002596 49.24 59.34 53.71 0.57 0.51 0.62 1.80 1.41 1.81
GPR68 ENST00000531499 49.25 75.47 63.54 0.57 0.44 0.49 1.80 0.90 1.39
AUH ENST00000375731 49.25 53.22 50.26 0.57 0.66 0.65 1.80 1.75 1.92
NANS ENST00000210444 49.26 72.97 61.86 0.57 0.51 0.47 1.80 1.03 1.46
PPEF2 ENST00000286719 49.26 51.88 49.49 0.57 0.59 0.67 1.80 1.86 1.83
HMGCLL1 ENST00000398661 49.27 58.84 53.46 0.57 0.54 0.63 1.80 1.41 1.82
PCDHAC1 ENST00000253807 49.27 57.15 52.53 0.57 0.56 0.61 1.81 1.50 1.90
SSTR3 ENST00000328544 49.28 77.14 64.51 0.57 0.42 0.51 1.81 0.78 1.34
ZNF512B ENST00000450537 49.28 6.06 25.79 0.57 2.81 1.02 1.80 0.35 1.23
CCDC102A ENST00000258214 49.29 45.68 46.17 0.57 0.75 0.67 1.80 2.01 1.96
PAQR7 ENST00000374296 49.29 68.95 59.37 0.57 0.54 0.49 1.81 1.16 1.70
NVL ENST00000281701 49.30 49.89 48.51 0.57 0.66 0.68 1.81 2.01 1.86
PLA2R1 ENST00000283243 49.31 46.05 46.38 0.57 0.77 0.67 1.81 2.04 1.90
GNA15 ENST00000262958 49.31 38.35 42.06 0.57 0.75 0.71 1.80 1.72 1.99
IFT20 ENST00000585089 49.32 47.25 47.01 0.57 0.66 0.70 1.80 2.00 1.88
NTS ENST00000256010 49.32 84.55 68.98 0.57 0.29 0.46 1.80 0.42 1.03
RHPN2 ENST00000254260 49.33 39.23 42.53 0.57 0.70 0.68 1.81 1.64 2.01

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