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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
OR4K2 ENST00000298642 75.93 93.01 87.61 0.34 0.28 0.27 0.76 0.30 0.31
OSGIN1 ENST00000361711 75.94 75.10 78.76 0.34 0.51 0.39 0.76 0.91 0.53
OR5I1 ENST00000301532 75.94 95.99 89.08 0.34 0.22 0.19 0.76 0.20 0.26
BEX2 ENST00000536889 75.95 69.89 75.92 0.34 0.53 0.38 0.76 1.15 0.62
EMB ENST00000303221 75.95 79.17 80.90 0.34 0.39 0.39 0.76 0.69 0.51
BOLA1 ENST00000369153 75.96 88.04 85.35 0.34 0.25 0.34 0.76 0.38 0.36
MTG2 ENST00000370823 75.96 41.74 58.96 0.34 0.61 0.49 0.76 1.79 1.65
IRX6 ENST00000290552 75.97 75.86 79.24 0.34 0.43 0.38 0.76 0.88 0.54
ZNF699 ENST00000591998 75.97 46.37 61.92 0.34 0.73 0.48 0.76 2.04 1.45
SIRT3 ENST00000382743 75.98 57.29 68.64 0.34 0.56 0.47 0.76 1.49 1.05
DMRT3 ENST00000190165 75.98 66.59 74.13 0.34 0.54 0.39 0.76 1.22 0.69
PGAM5 ENST00000498926 75.99 66.15 73.85 0.34 0.53 0.42 0.76 1.20 0.71
OPALIN ENST00000371172 75.99 77.30 79.99 0.34 0.42 0.35 0.76 0.77 0.52
ITLN2 ENST00000368029 76.00 63.32 72.36 0.34 0.47 0.44 0.76 1.31 0.83
PLEKHA4 ENST00000263265 76.00 46.01 61.74 0.34 0.77 0.46 0.76 2.02 1.46
C1D ENST00000355848 76.01 70.35 76.25 0.34 0.52 0.37 0.76 1.08 0.61
ZNF852 ENST00000436261 76.01 67.08 74.46 0.34 0.54 0.40 0.76 1.23 0.69
HLA-DPB1 ENST00000418931 76.02 81.33 82.04 0.34 0.33 0.35 0.77 0.54 0.46
ROPN1L ENST00000503804 76.02 81.90 82.35 0.34 0.35 0.33 0.77 0.51 0.44
C11orf48 ENST00000532208 76.03 67.15 74.51 0.34 0.54 0.40 0.77 1.22 0.68
C4orf21 ENST00000505019 76.03 55.31 67.48 0.34 0.57 0.52 0.77 1.61 1.14
OR1D2 ENST00000331459 76.04 81.37 82.08 0.34 0.33 0.35 0.77 0.54 0.46
HLA-DQA2 ENST00000374940 76.04 82.20 82.54 0.34 0.34 0.32 0.78 0.52 0.43
GCNT2 ENST00000379597 76.05 65.14 73.37 0.34 0.49 0.42 0.78 1.24 0.78
OR6C4 ENST00000394256 76.05 97.07 89.68 0.34 0.24 0.18 0.78 0.19 0.23

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