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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
SLC12A4 ENST00000422611 39.65 36.55 36.23 0.90 0.78 0.86 1.75 1.63 1.83
ZRSR2 ENST00000307771 39.65 3.03 19.34 0.90 3.47 1.53 1.75 0.28 0.85
PROSC ENST00000328195 39.66 36.33 36.10 0.90 0.82 0.89 1.74 1.62 1.80
USP53 ENST00000450251 39.66 41.74 39.05 0.90 0.61 0.78 1.73 1.78 2.06
ERCC6L2 ENST00000288985 39.67 35.95 35.93 0.90 0.80 0.86 1.74 1.58 1.78
C20orf27 ENST00000217195 39.67 70.97 54.87 0.90 0.49 0.51 1.75 1.05 1.74
RPF2 ENST00000441448 39.68 35.29 35.62 0.90 0.76 0.85 1.74 1.58 1.77
BDH2 ENST00000296424 39.68 73.85 56.59 0.90 0.53 0.52 1.74 1.03 1.70
TMEM200A ENST00000392429 39.69 23.76 29.92 0.90 1.38 0.86 1.74 0.93 1.44
PTPDC1 ENST00000288976 39.69 31.79 33.92 0.90 0.94 0.90 1.73 1.48 1.73
PEX13 ENST00000295030 39.70 57.06 47.10 0.90 0.56 0.68 1.73 1.52 1.89
BROX ENST00000340934 39.70 58.55 47.96 0.89 0.54 0.67 1.74 1.41 1.88
NBEAL1 ENST00000449802 39.71 32.89 34.52 0.89 0.82 0.90 1.73 1.45 1.77
NUMA1 ENST00000393695 39.71 5.98 20.98 0.89 2.81 1.43 1.73 0.35 0.88
PHLPP2 ENST00000568954 39.72 26.93 31.54 0.89 1.23 0.86 1.73 1.12 1.56
NRAP ENST00000359988 39.72 54.50 45.83 0.89 0.59 0.68 1.73 1.66 1.97
KL ENST00000380099 39.73 29.22 32.67 0.89 1.13 0.86 1.73 1.35 1.63
CEP55 ENST00000371485 39.73 60.52 49.01 0.89 0.52 0.72 1.74 1.41 1.84
PSMB4 ENST00000290541 39.74 44.49 40.37 0.89 0.63 0.80 1.74 1.98 2.02
SAMD14 ENST00000503131 39.74 36.45 36.23 0.89 0.82 0.86 1.73 1.65 1.84
MSS51 ENST00000299432 39.75 74.52 57.00 0.89 0.53 0.51 1.73 1.00 1.70
CD74 ENST00000009530 39.76 28.81 32.47 0.89 1.14 0.89 1.73 1.30 1.63
BCAP31 ENST00000458587 39.76 34.55 35.38 0.89 0.80 0.87 1.73 1.55 1.77
FARS2 ENST00000324331 39.77 64.50 51.22 0.89 0.48 0.63 1.74 1.22 1.92
CYP19A1 ENST00000396402 39.77 52.43 44.67 0.89 0.65 0.62 1.74 1.83 2.06

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