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
FAM218A ENST00000513876 96.46 99.42 99.49 0.10 0.16 0.11 0.11 0.12 0.05
CST11 ENST00000377009 96.47 90.57 96.25 0.10 0.25 0.07 0.11 0.37 0.09
MUC20 ENST00000447234 96.47 52.07 77.49 0.10 0.59 0.35 0.11 1.85 0.57
MRPL36 ENST00000508987 96.48 98.82 99.36 0.10 0.16 0.11 0.11 0.14 0.04
PRB1 ENST00000500254 96.48 94.66 98.03 0.10 0.23 0.09 0.11 0.24 0.05
GSDMB ENST00000418519 96.49 58.89 81.03 0.10 0.53 0.39 0.11 1.42 0.50
ZNF776 ENST00000317178 96.49 91.38 96.73 0.10 0.23 0.08 0.11 0.33 0.08
MS4A4A ENST00000337908 96.50 74.81 88.76 0.10 0.53 0.19 0.11 0.95 0.28
OBP2A ENST00000539850 96.50 84.58 93.25 0.10 0.29 0.14 0.11 0.42 0.15
C4BPA ENST00000367070 96.51 20.73 58.72 0.10 1.46 0.52 0.11 0.81 1.65
GLT6D1 ENST00000371763 96.51 67.21 85.20 0.10 0.54 0.34 0.11 1.22 0.37
C5orf38 ENST00000334000 96.52 75.39 89.07 0.10 0.47 0.19 0.11 0.89 0.26
KIR3DL1 ENST00000391728 96.52 88.09 95.06 0.10 0.24 0.09 0.11 0.38 0.10
C15orf53 ENST00000318792 96.53 95.04 98.16 0.10 0.23 0.09 0.11 0.21 0.05
LCN1 ENST00000263598 96.53 90.75 96.38 0.10 0.25 0.07 0.11 0.35 0.09
GP6 ENST00000310373 96.54 83.36 92.70 0.10 0.27 0.14 0.11 0.48 0.15
TCEB2 ENST00000262306 96.54 72.96 87.86 0.10 0.51 0.24 0.11 1.03 0.32
PRAMEF10 ENST00000235347 96.55 82.55 92.23 0.10 0.34 0.14 0.11 0.51 0.16
ZNF587 ENST00000339656 96.55 84.85 93.47 0.10 0.27 0.11 0.11 0.42 0.15
PRAMEF4 ENST00000235349 96.56 93.20 97.48 0.10 0.28 0.08 0.11 0.30 0.07
GLYATL1 ENST00000300079 96.57 54.07 78.57 0.10 0.65 0.38 0.11 1.69 0.55
SH3D21 ENST00000453908 96.57 52.30 77.64 0.11 0.62 0.38 0.11 1.83 0.55
LILRA6 ENST00000396365 96.58 46.74 74.59 0.11 0.72 0.40 0.11 1.97 0.68
C19orf48 ENST00000598463 96.58 98.96 99.41 0.11 0.17 0.11 0.11 0.15 0.05
ZNF611 ENST00000543227 96.59 80.69 91.50 0.11 0.37 0.15 0.11 0.56 0.18

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.