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
SETD5 ENST00000402198 12.14 7.84 7.38 1.67 2.56 2.80 0.61 0.44 0.34
OPA1 ENST00000361908 12.15 10.58 8.71 1.67 2.15 2.51 0.61 0.51 0.37
MED13 ENST00000397786 12.15 0.02 3.51 1.67 4.11 3.84 0.60 0.26 0.23
AP3S1 ENST00000316788 12.16 80.13 44.74 1.67 0.37 0.63 0.60 0.60 2.06
SIPA1L1 ENST00000555818 12.16 3.86 5.25 1.67 3.30 3.56 0.61 0.31 0.26
TRA2A ENST00000297071 12.17 37.68 23.05 1.67 0.78 1.21 0.61 1.70 0.99
HLF ENST00000226067 12.17 13.37 10.34 1.67 2.05 2.19 0.61 0.59 0.43
SOS2 ENST00000216373 12.18 9.32 8.11 1.67 2.48 2.58 0.60 0.48 0.37
CCNT2 ENST00000264157 12.18 15.23 11.38 1.68 1.89 2.19 0.60 0.67 0.45
ACIN1 ENST00000262710 12.19 6.36 6.65 1.68 2.67 3.01 0.60 0.37 0.32
GAPVD1 ENST00000394105 12.19 1.24 4.05 1.67 3.99 3.75 0.60 0.27 0.23
C6orf62 ENST00000378119 12.20 8.26 7.58 1.67 2.54 2.75 0.59 0.45 0.33
FUBP3 ENST00000319725 12.20 16.68 12.00 1.66 1.71 2.29 0.59 0.71 0.47
ATRN ENST00000262919 12.21 4.71 5.71 1.67 3.27 3.31 0.59 0.31 0.28
CYB561D2 ENST00000418577 12.22 77.54 43.23 1.67 0.42 0.65 0.59 0.79 1.99
C12orf23 ENST00000280756 12.22 88.77 49.35 1.67 0.25 0.70 0.59 0.36 1.84
HSF2 ENST00000368455 12.23 13.04 10.21 1.67 2.07 2.21 0.59 0.59 0.42
GRHL1 ENST00000324907 12.23 20.87 14.28 1.67 1.42 2.00 0.59 0.84 0.60
CLDN12 ENST00000535571 12.24 59.14 33.85 1.67 0.49 0.89 0.59 1.44 1.73
B4GALT5 ENST00000371711 12.24 3.04 4.92 1.68 3.46 3.69 0.59 0.28 0.25
ICMT ENST00000343813 12.25 21.74 14.77 1.68 1.46 1.96 0.59 0.81 0.62
FAM120C ENST00000375180 12.25 0.70 3.83 1.68 4.09 3.77 0.59 0.28 0.24
FOSL2 ENST00000264716 12.26 8.56 7.75 1.68 2.52 2.66 0.60 0.47 0.33
CYBB ENST00000378588 12.26 5.65 6.21 1.68 2.97 3.15 0.60 0.33 0.32
TP63 ENST00000264731 12.27 10.73 8.90 1.68 2.14 2.49 0.60 0.51 0.38

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.