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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
OR1B1 ENST00000304833 70.77 88.81 83.16 0.49 0.25 0.29 0.90 0.35 0.40
IMPG1 ENST00000369950 70.77 70.15 73.20 0.49 0.53 0.43 0.89 1.12 0.79
OR51E2 ENST00000396950 70.78 84.28 80.83 0.49 0.28 0.39 0.89 0.44 0.51
PLEKHF1 ENST00000436066 70.78 54.27 63.77 0.49 0.62 0.49 0.89 1.70 1.38
PPM1F ENST00000263212 70.79 40.69 55.41 0.49 0.63 0.49 0.88 1.77 1.71
GPR123 ENST00000392607 70.79 37.50 53.55 0.49 0.78 0.63 0.88 1.67 1.80
ADAMTS20 ENST00000389420 70.80 44.77 57.81 0.48 0.67 0.51 0.88 1.97 1.66
UBXN6 ENST00000301281 70.80 44.80 57.80 0.48 0.68 0.51 0.88 1.97 1.68
FAM83H ENST00000388913 70.81 16.86 42.03 0.47 1.66 0.70 0.88 0.71 1.98
POLI ENST00000579534 70.81 45.53 58.25 0.47 0.72 0.47 0.88 1.99 1.65
PLSCR5 ENST00000443512 70.82 80.28 78.79 0.47 0.37 0.39 0.88 0.58 0.52
KLK12 ENST00000250351 70.82 73.91 75.27 0.47 0.53 0.37 0.89 1.02 0.67
EXPH5 ENST00000265843 70.83 49.85 60.97 0.47 0.66 0.43 0.89 2.02 1.58
FUK ENST00000288078 70.83 60.53 67.49 0.47 0.52 0.51 0.89 1.41 1.14
ASAH2C ENST00000426610 70.84 53.09 62.95 0.47 0.66 0.51 0.88 1.77 1.40
CABP4 ENST00000325656 70.84 81.10 79.28 0.47 0.35 0.38 0.88 0.55 0.54
C17orf59 ENST00000389017 70.85 50.94 61.62 0.47 0.65 0.46 0.87 1.94 1.48
PAM16 ENST00000318059 70.85 45.36 58.18 0.47 0.68 0.48 0.87 1.99 1.65
GLB1L2 ENST00000535456 70.86 63.72 69.45 0.47 0.49 0.43 0.87 1.23 0.98
KRBA2 ENST00000331336 70.86 72.62 74.67 0.47 0.47 0.40 0.87 1.05 0.68
FAM71F2 ENST00000480462 70.87 48.81 60.30 0.47 0.63 0.47 0.87 2.02 1.59
SLC9B1 ENST00000296422 70.87 55.96 64.82 0.47 0.49 0.51 0.87 1.56 1.32
SDK1 ENST00000404826 70.88 19.08 43.34 0.47 1.52 0.63 0.87 0.76 2.01
HIST1H2AH ENST00000377459 70.88 96.48 86.84 0.47 0.22 0.29 0.88 0.19 0.32
COQ7 ENST00000321998 70.89 79.95 78.68 0.47 0.37 0.38 0.88 0.61 0.54

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