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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
LIPJ ENST00000371939 81.61 68.22 78.16 0.30 0.52 0.39 0.60 1.21 0.55
C2orf61 ENST00000445927 81.62 64.98 76.40 0.30 0.49 0.38 0.60 1.24 0.61
TMEM129 ENST00000382936 81.62 87.90 87.89 0.30 0.25 0.24 0.60 0.38 0.32
RLN3 ENST00000431365 81.63 84.42 86.25 0.32 0.29 0.33 0.60 0.44 0.33
AKR1B15 ENST00000457545 81.63 95.27 91.36 0.32 0.23 0.15 0.60 0.21 0.18
NPEPL1 ENST00000356091 81.64 58.56 72.84 0.32 0.54 0.42 0.60 1.41 0.80
AGPAT2 ENST00000371696 81.64 82.61 85.49 0.32 0.34 0.33 0.60 0.50 0.35
FAM216B ENST00000537894 81.65 79.42 83.88 0.32 0.38 0.35 0.60 0.67 0.43
ZNF467 ENST00000302017 81.65 69.48 78.80 0.32 0.54 0.39 0.60 1.12 0.52
TIAF1 ENST00000359450 81.66 99.45 93.30 0.32 0.16 0.13 0.60 0.12 0.15
MLPH ENST00000264605 81.66 48.74 66.94 0.32 0.63 0.53 0.60 2.00 1.19
CCDC177 ENST00000543986 81.67 98.14 92.30 0.32 0.20 0.14 0.60 0.16 0.15
DPH7 ENST00000277540 81.67 69.61 78.92 0.32 0.53 0.39 0.60 1.10 0.52
RILP ENST00000301336 81.68 85.30 86.66 0.32 0.25 0.30 0.60 0.46 0.33
KRTAP4-11 ENST00000391413 81.68 87.47 87.73 0.32 0.23 0.24 0.60 0.40 0.32
TFB2M ENST00000366514 81.69 54.17 70.16 0.32 0.63 0.43 0.60 1.69 0.90
OR4K17 ENST00000315543 81.70 90.43 89.16 0.32 0.25 0.19 0.60 0.37 0.25
SELO ENST00000380903 81.70 87.19 87.58 0.32 0.20 0.27 0.60 0.41 0.31
GPRIN2 ENST00000374314 81.71 76.03 82.24 0.32 0.43 0.35 0.60 0.86 0.44
TEX33 ENST00000405091 81.71 81.45 84.94 0.32 0.33 0.34 0.60 0.55 0.40
OCM ENST00000242104 81.72 96.24 91.77 0.32 0.22 0.15 0.60 0.19 0.18
SHROOM1 ENST00000378679 81.72 28.39 54.60 0.32 1.16 0.56 0.60 1.23 1.74
ZNF708 ENST00000356929 81.73 85.18 86.64 0.32 0.25 0.30 0.60 0.45 0.33
ALS2CR11 ENST00000439140 81.73 39.43 61.26 0.32 0.70 0.44 0.60 1.64 1.48
MPPE1 ENST00000588072 81.74 67.23 77.67 0.32 0.54 0.38 0.60 1.22 0.55

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