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
HIST1H4B ENST00000377364 85.87 95.86 93.63 0.27 0.22 0.13 0.45 0.20 0.15
KRTAP4-9 ENST00000391415 85.88 95.52 93.44 0.27 0.23 0.11 0.45 0.21 0.15
LDLRAD2 ENST00000344642 85.88 62.67 77.48 0.27 0.51 0.35 0.45 1.31 0.57
NCR3LG1 ENST00000338965 85.89 62.47 77.34 0.27 0.53 0.35 0.45 1.31 0.58
APOC3 ENST00000227667 85.89 89.01 90.52 0.27 0.27 0.14 0.45 0.35 0.21
KRTAP19-8 ENST00000382822 85.90 98.20 94.87 0.27 0.20 0.09 0.45 0.15 0.11
RHNO1 ENST00000489288 85.90 76.42 84.52 0.27 0.44 0.33 0.45 0.85 0.40
ANKRD53 ENST00000360589 85.91 74.82 83.75 0.27 0.53 0.34 0.45 0.95 0.41
ZNF557 ENST00000414706 85.91 50.07 70.24 0.27 0.67 0.43 0.45 1.99 0.91
ANKUB1 ENST00000446160 85.92 63.44 77.89 0.27 0.49 0.38 0.45 1.27 0.54
TNFRSF6B ENST00000369996 85.93 87.76 89.92 0.27 0.24 0.18 0.44 0.37 0.23
OGFR ENST00000290291 85.93 37.34 62.47 0.25 0.76 0.48 0.44 1.65 1.40
ZNF414 ENST00000393927 85.94 37.57 62.67 0.25 0.80 0.51 0.44 1.69 1.39
C19orf52 ENST00000270502 85.94 85.54 88.88 0.25 0.27 0.19 0.44 0.44 0.28
EMC10 ENST00000334976 85.95 81.64 86.99 0.25 0.33 0.28 0.44 0.52 0.30
ZNF784 ENST00000325351 85.95 26.44 55.85 0.25 1.16 0.51 0.44 1.10 1.75
TRAM1L1 ENST00000310754 85.96 75.02 83.85 0.25 0.52 0.34 0.44 0.92 0.42
CLEC11A ENST00000250340 85.96 61.74 76.98 0.25 0.57 0.37 0.44 1.37 0.61
CHIC1 ENST00000373502 85.97 24.55 54.83 0.25 1.30 0.53 0.44 1.04 1.74
REG3G ENST00000272324 85.97 89.62 90.87 0.25 0.27 0.15 0.44 0.37 0.20
RNF39 ENST00000244360 85.98 66.15 79.35 0.25 0.53 0.39 0.44 1.20 0.54
SOX8 ENST00000293894 85.98 26.17 55.76 0.25 1.19 0.52 0.44 1.08 1.74
ABCA10 ENST00000269081 85.99 53.21 72.29 0.25 0.66 0.43 0.44 1.75 0.81
SLC25A41 ENST00000321510 85.99 79.14 85.86 0.25 0.39 0.33 0.44 0.69 0.33
PEBP4 ENST00000256404 86.00 76.60 84.63 0.25 0.42 0.34 0.44 0.83 0.40

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.