GeVIR Banner

Export Results to CSV Clear Search

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
KCNE1 ENST00000337385 75.80 95.13 88.57 0.34 0.23 0.22 0.76 0.21 0.28
C2orf62 ENST00000289388 75.81 64.74 73.02 0.34 0.48 0.42 0.76 1.24 0.80
MYBPC2 ENST00000357701 75.81 52.74 65.88 0.34 0.66 0.51 0.76 1.79 1.24
NCF1 ENST00000289473 75.82 57.22 68.50 0.33 0.56 0.47 0.76 1.49 1.06
KRT32 ENST00000225899 75.82 88.18 85.35 0.33 0.23 0.34 0.76 0.37 0.36
C2orf53 ENST00000335524 75.83 89.40 85.89 0.33 0.27 0.33 0.77 0.37 0.33
CCR3 ENST00000545097 75.83 73.98 78.14 0.33 0.53 0.39 0.77 1.02 0.55
CYB5R2 ENST00000533558 75.84 82.27 82.44 0.33 0.34 0.33 0.76 0.52 0.44
PRDM9 ENST00000296682 75.84 68.44 75.07 0.33 0.52 0.39 0.76 1.21 0.67
ATAD3A ENST00000378755 75.85 45.61 61.41 0.33 0.73 0.44 0.76 2.00 1.48
PLB1 ENST00000327757 75.85 66.49 73.97 0.33 0.57 0.40 0.76 1.21 0.69
ZNF37A ENST00000361085 75.86 66.26 73.84 0.33 0.53 0.42 0.76 1.20 0.71
COX16 ENST00000389912 75.86 88.88 85.69 0.33 0.25 0.33 0.75 0.35 0.34
CELA3B ENST00000337107 75.87 84.14 83.34 0.33 0.27 0.32 0.75 0.45 0.40
C1orf168 ENST00000343433 75.87 86.01 84.23 0.33 0.25 0.34 0.75 0.43 0.42
TUBGCP6 ENST00000248846 75.88 50.33 64.36 0.33 0.66 0.51 0.75 1.96 1.34
TRIM65 ENST00000269383 75.88 89.22 85.85 0.33 0.27 0.33 0.75 0.36 0.33
OR52J3 ENST00000380370 75.89 94.44 88.34 0.33 0.23 0.22 0.75 0.24 0.30
PCDHB3 ENST00000231130 75.89 67.85 74.78 0.33 0.52 0.40 0.75 1.17 0.66
SLC47A2 ENST00000325411 75.90 62.06 71.49 0.33 0.56 0.46 0.75 1.37 0.85
HERC6 ENST00000264346 75.91 48.13 63.06 0.33 0.63 0.51 0.75 1.98 1.39
PRR5-ARHGAP8 ENST00000352766 75.91 82.59 82.67 0.33 0.34 0.32 0.75 0.51 0.43
TMEM187 ENST00000369982 75.92 86.04 84.28 0.33 0.27 0.34 0.75 0.43 0.42
OR12D3 ENST00000396806 75.92 90.81 86.57 0.33 0.25 0.30 0.76 0.35 0.33
OR1D5 ENST00000575751 75.93 73.94 78.19 0.34 0.53 0.39 0.76 1.02 0.55

Cookies disclaimer

I agree Our site saves small pieces of text information (cookies) on your device in order to deliver better content and for statistical purposes. You can disable the usage of cookies by changing the settings of your browser. By browsing our website without changing the browser settings you grant us permission to store that information on your device.