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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
MROH2B ENST00000399564 66.12 51.58 58.95 0.59 0.62 0.49 1.07 1.87 1.65
BIRC5 ENST00000301633 66.12 57.65 62.88 0.59 0.56 0.51 1.07 1.48 1.40
ATP5J2-PTCD1 ENST00000413834 66.13 65.02 67.37 0.59 0.51 0.52 1.06 1.24 1.15
PTCD1 ENST00000555673 66.13 65.07 67.40 0.59 0.51 0.52 1.06 1.24 1.15
C1orf111 ENST00000367935 66.14 92.65 82.77 0.59 0.29 0.32 1.06 0.31 0.42
HDHD3 ENST00000238379 66.14 76.76 74.31 0.59 0.40 0.40 1.06 0.83 0.69
SFTA3 ENST00000518529 66.15 52.12 59.39 0.59 0.61 0.49 1.06 1.85 1.70
GALNT15 ENST00000339732 66.15 73.30 72.42 0.59 0.56 0.44 1.06 1.02 0.83
MREG ENST00000263268 66.16 78.79 75.40 0.59 0.42 0.37 1.06 0.71 0.65
CCDC83 ENST00000280245 66.16 58.16 63.28 0.59 0.54 0.49 1.06 1.45 1.36
PSRC1 ENST00000369909 66.17 70.91 70.90 0.59 0.49 0.43 1.06 1.07 0.86
LRRC30 ENST00000383467 66.17 92.03 82.53 0.59 0.24 0.32 1.06 0.33 0.43
LCORL ENST00000382226 66.18 12.89 37.76 0.59 2.07 0.84 1.06 0.59 2.01
VRK3 ENST00000599538 66.18 59.12 63.94 0.59 0.49 0.51 1.06 1.44 1.39
PTGES2 ENST00000338961 66.19 74.55 73.11 0.59 0.53 0.42 1.06 1.00 0.79
SHPK ENST00000225519 66.19 71.18 71.14 0.58 0.52 0.43 1.06 1.06 0.87
LRRC18 ENST00000374160 66.20 93.81 83.38 0.58 0.27 0.33 1.06 0.26 0.40
PCDHA1 ENST00000504120 66.21 49.36 57.77 0.58 0.65 0.49 1.06 2.01 1.67
OR6X1 ENST00000327930 66.21 81.29 76.88 0.58 0.33 0.35 1.07 0.54 0.60
TMEM143 ENST00000293261 66.22 76.36 74.10 0.58 0.43 0.39 1.07 0.86 0.69
GPR114 ENST00000340339 66.22 26.50 45.01 0.58 1.18 0.70 1.07 1.11 2.05
SHF ENST00000290894 66.23 24.81 43.93 0.58 1.33 0.61 1.08 1.05 2.02
CYP2S1 ENST00000310054 66.23 48.02 56.99 0.58 0.63 0.49 1.07 2.01 1.70
FAM161B ENST00000286544 66.24 57.94 63.17 0.58 0.57 0.49 1.08 1.46 1.37
CMYA5 ENST00000446378 66.24 49.04 57.61 0.58 0.66 0.51 1.08 2.03 1.68

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