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
AP000350.4 ENST00000406213 97.73 86.18 94.70 0.10 0.27 0.09 0.10 0.42 0.11
TEX19 ENST00000333437 98.34 97.84 99.56 0.09 0.21 0.12 0.10 0.17 0.05
ZNF534 ENST00000332323 97.73 93.97 98.19 0.10 0.25 0.09 0.10 0.26 0.05
ARMS2 ENST00000528446 98.33 96.64 99.24 0.09 0.23 0.11 0.10 0.20 0.04
XAGE3 ENST00000346279 97.72 71.75 87.86 0.10 0.51 0.24 0.10 1.07 0.32
ZNF878 ENST00000547628 98.33 75.53 90.01 0.09 0.44 0.18 0.10 0.90 0.22
TCP10 ENST00000397829 97.72 67.95 86.07 0.10 0.52 0.33 0.10 1.17 0.33
C22orf34 ENST00000400023 98.32 85.90 94.87 0.09 0.28 0.09 0.10 0.43 0.11
GCSAML ENST00000366488 97.71 63.98 84.11 0.10 0.48 0.34 0.10 1.20 0.42
CRISP3 ENST00000433368 98.32 62.35 83.74 0.09 0.53 0.34 0.10 1.33 0.41
H1FOO ENST00000324382 97.71 52.73 78.46 0.10 0.66 0.38 0.10 1.79 0.54
NKG2-E ENST00000539033 98.31 86.87 95.30 0.09 0.22 0.08 0.10 0.41 0.10
PALM3 ENST00000340790 97.70 32.49 66.83 0.10 0.86 0.53 0.10 1.48 1.20
C8orf86 ENST00000358138 98.31 86.94 95.37 0.09 0.22 0.08 0.10 0.40 0.10
C1orf170 ENST00000433179 97.70 86.60 94.91 0.10 0.24 0.09 0.10 0.40 0.11
SLC22A14 ENST00000273173 97.69 69.72 86.87 0.10 0.53 0.29 0.10 1.13 0.31
FCER1A ENST00000368115 98.30 75.29 89.89 0.09 0.49 0.18 0.10 0.90 0.23
C19orf18 ENST00000314391 97.69 83.64 93.38 0.10 0.27 0.11 0.10 0.47 0.15
ZNF320 ENST00000595635 98.30 79.48 91.73 0.09 0.38 0.14 0.10 0.66 0.18
ZNF57 ENST00000306908 97.68 81.36 92.21 0.10 0.33 0.14 0.10 0.54 0.16
APOBEC3G ENST00000407997 98.29 85.89 94.80 0.09 0.28 0.09 0.10 0.43 0.11
RFPL1 ENST00000354373 97.68 87.62 95.40 0.10 0.23 0.08 0.10 0.35 0.11
RP11-404P21.8 ENST00000553811 98.29 93.96 98.40 0.09 0.25 0.10 0.10 0.26 0.05
AIM2 ENST00000368130 97.67 84.24 93.76 0.10 0.28 0.10 0.10 0.44 0.13
SPRR3 ENST00000331860 98.28 98.33 99.56 0.09 0.21 0.12 0.10 0.14 0.05

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.