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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
C6orf163 ENST00000388923 72.32 50.44 62.19 0.34 0.65 0.48 0.80 1.95 1.45
DCDC2B ENST00000409358 72.32 69.31 73.60 0.34 0.56 0.40 0.80 1.14 0.74
POC5 ENST00000428202 72.33 49.33 61.55 0.34 0.65 0.46 0.80 2.02 1.48
ZDHHC1 ENST00000348579 72.33 60.31 68.31 0.33 0.53 0.49 0.80 1.39 1.07
TTC23 ENST00000394132 72.34 87.36 83.22 0.33 0.23 0.29 0.80 0.41 0.40
AVPI1 ENST00000370626 72.34 93.13 85.97 0.33 0.28 0.33 0.80 0.30 0.33
SCEL ENST00000349847 72.35 53.75 64.33 0.33 0.63 0.51 0.80 1.70 1.35
SPAG16 ENST00000331683 72.35 86.45 82.80 0.33 0.24 0.32 0.80 0.42 0.42
NEUROG3 ENST00000242462 72.36 94.94 86.82 0.33 0.23 0.29 0.80 0.22 0.32
PIGN ENST00000357637 72.36 53.13 64.03 0.33 0.67 0.53 0.80 1.77 1.39
ASAH1 ENST00000381733 72.37 63.65 70.29 0.33 0.49 0.43 0.79 1.23 0.91
SSTR5 ENST00000293897 72.37 82.74 80.88 0.33 0.33 0.39 0.79 0.50 0.51
LRRC19 ENST00000380055 72.38 89.50 84.22 0.33 0.27 0.34 0.79 0.36 0.42
OR9K2 ENST00000305377 72.38 95.89 87.35 0.33 0.22 0.28 0.79 0.20 0.31
HIST1H2AB ENST00000259791 72.39 95.80 87.28 0.33 0.22 0.28 0.79 0.20 0.31
RINL ENST00000591812 72.39 38.42 54.99 0.33 0.75 0.52 0.79 1.70 1.75
ISYNA1 ENST00000338128 72.40 44.32 58.41 0.33 0.61 0.52 0.79 1.95 1.65
CNBD2 ENST00000349339 72.40 66.23 71.94 0.32 0.53 0.43 0.79 1.20 0.81
MRI1 ENST00000040663 72.41 56.07 65.85 0.32 0.51 0.51 0.79 1.55 1.25
CENPT ENST00000562787 72.41 43.02 57.71 0.32 0.61 0.49 0.79 1.89 1.68
MRPL18 ENST00000367034 72.42 70.48 74.32 0.32 0.52 0.40 0.79 1.08 0.69
SAYSD1 ENST00000229903 72.42 84.61 81.88 0.32 0.28 0.37 0.79 0.42 0.46
NOMO1 ENST00000287667 72.43 54.64 64.98 0.32 0.58 0.49 0.79 1.65 1.32
ABHD14A ENST00000273596 72.43 75.90 77.33 0.32 0.43 0.35 0.79 0.88 0.58
DUSP2 ENST00000288943 72.44 59.61 67.94 0.32 0.52 0.51 0.79 1.41 1.10

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