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
ZNF213 ENST00000396878 58.63 56.45 57.47 0.57 0.52 0.51 1.51 1.54 1.65
KNTC1 ENST00000333479 58.63 40.70 48.54 0.57 0.63 0.68 1.51 1.77 1.85
TTC38 ENST00000381031 58.64 60.01 59.66 0.57 0.53 0.49 1.52 1.37 1.67
CTSO ENST00000433477 58.64 74.13 68.35 0.57 0.53 0.49 1.52 1.03 1.07
OR5C1 ENST00000373680 58.65 87.37 76.01 0.57 0.23 0.38 1.51 0.41 0.62
HOXA9 ENST00000343483 58.65 83.11 73.68 0.57 0.29 0.42 1.51 0.49 0.72
JAM2 ENST00000400532 58.66 36.63 46.30 0.57 0.77 0.67 1.51 1.65 1.91
MIA3 ENST00000344922 58.66 15.56 35.35 0.57 1.87 0.87 1.51 0.67 1.77
KRT2 ENST00000309680 58.67 33.21 44.47 0.57 0.82 0.61 1.50 1.50 2.04
WISP3 ENST00000361714 58.67 48.40 52.86 0.57 0.63 0.61 1.50 2.01 1.87
AP5S1 ENST00000246041 58.68 87.93 76.44 0.57 0.25 0.38 1.50 0.37 0.61
BBS10 ENST00000393262 58.68 73.73 68.20 0.57 0.52 0.49 1.50 1.03 1.08
MMADHC ENST00000428879 58.69 54.41 56.33 0.57 0.62 0.49 1.50 1.66 1.75
CHRNA9 ENST00000310169 58.70 55.26 56.83 0.57 0.57 0.52 1.50 1.62 1.69
KNSTRN ENST00000249776 58.70 58.87 58.90 0.57 0.53 0.49 1.50 1.42 1.65
SPHKAP ENST00000392056 58.71 13.13 34.09 0.57 2.07 0.91 1.50 0.60 1.74
MEF2B ENST00000162023 58.71 55.56 57.03 0.57 0.54 0.51 1.50 1.60 1.70
PARP4 ENST00000381989 58.72 45.84 51.40 0.57 0.73 0.63 1.50 2.01 1.90
MCHR1 ENST00000249016 58.72 73.74 68.19 0.56 0.52 0.49 1.50 1.03 1.08
PTGIS ENST00000244043 58.73 59.89 59.61 0.56 0.53 0.49 1.50 1.36 1.68
CECR5 ENST00000336737 58.73 74.07 68.38 0.56 0.53 0.48 1.50 1.03 1.05
PDE6B ENST00000496514 58.74 65.98 63.53 0.56 0.56 0.49 1.50 1.23 1.39
PCDHA5 ENST00000529859 58.74 48.61 53.10 0.56 0.63 0.61 1.50 2.01 1.87
NDUFS5 ENST00000372969 58.75 73.63 68.17 0.56 0.52 0.49 1.50 1.03 1.08
GLRX5 ENST00000331334 58.75 34.29 45.19 0.56 0.85 0.70 1.50 1.56 2.00

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.