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
SLC2A9 ENST00000264784 61.60 63.20 63.60 0.68 0.47 0.49 1.29 1.31 1.39
SLC35G6 ENST00000412468 61.60 75.04 70.63 0.68 0.52 0.43 1.29 0.92 0.90
CSPG4 ENST00000308508 61.61 22.10 40.14 0.68 1.51 0.82 1.29 0.83 1.99
LAG3 ENST00000203629 61.61 25.92 41.99 0.68 1.21 0.68 1.29 1.09 1.99
NUDT6 ENST00000304430 61.62 52.85 57.15 0.68 0.65 0.52 1.29 1.80 1.69
MUM1L1 ENST00000337685 61.62 26.96 42.54 0.68 1.23 0.68 1.29 1.11 2.02
FANCB ENST00000398334 61.63 7.73 32.85 0.68 2.53 0.85 1.29 0.43 1.66
ACTBL2 ENST00000423391 61.63 96.26 82.31 0.68 0.22 0.33 1.29 0.19 0.44
GDF7 ENST00000272224 61.64 33.95 46.44 0.70 0.84 0.67 1.29 1.55 1.92
MCM7 ENST00000303887 61.64 70.02 67.68 0.70 0.53 0.52 1.29 1.14 1.13
MRPL14 ENST00000372014 61.65 88.08 78.06 0.70 0.24 0.39 1.29 0.38 0.55
KRTAP8-1 ENST00000329621 61.65 92.19 80.24 0.70 0.25 0.37 1.29 0.31 0.51
CYP8B1 ENST00000316161 61.66 66.63 65.75 0.70 0.54 0.51 1.29 1.22 1.25
TROAP ENST00000257909 61.67 46.25 53.37 0.70 0.73 0.62 1.29 2.04 1.84
RCL1 ENST00000381750 61.67 29.40 43.95 0.70 1.10 0.61 1.29 1.37 2.02
HIST3H2BB ENST00000369160 61.68 96.95 82.72 0.70 0.24 0.32 1.29 0.19 0.42
SYNPR ENST00000478300 61.68 48.30 54.53 0.70 0.63 0.56 1.29 1.99 1.74
KRT24 ENST00000264651 61.69 77.44 72.21 0.70 0.42 0.43 1.29 0.76 0.82
RTP2 ENST00000358241 61.69 86.40 77.22 0.71 0.25 0.35 1.29 0.42 0.59
COTL1 ENST00000262428 61.70 67.00 65.98 0.71 0.53 0.51 1.29 1.25 1.23
HIST1H2BL ENST00000377401 61.70 97.28 82.86 0.71 0.23 0.32 1.29 0.19 0.41
C11orf82 ENST00000533655 61.71 47.44 54.08 0.71 0.65 0.59 1.29 2.02 1.76
FAM193B ENST00000514747 61.71 11.07 34.61 0.71 2.09 0.90 1.29 0.53 1.76
NLGN4Y ENST00000355905 61.72 53.45 57.55 0.71 0.65 0.51 1.29 1.71 1.66
KCNA5 ENST00000252321 61.72 49.78 55.37 0.71 0.66 0.49 1.29 2.03 1.72

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.