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
NRIP1 ENST00000400202 41.97 10.60 24.33 0.78 2.15 1.09 1.75 0.51 1.07
CTSA ENST00000372484 41.98 45.66 42.03 0.78 0.75 0.70 1.75 2.01 1.99
IGSF3 ENST00000369483 41.98 17.80 28.09 0.78 1.52 0.81 1.75 0.73 1.29
LACE1 ENST00000368977 41.99 50.43 44.84 0.80 0.65 0.67 1.75 1.95 2.04
DPP6 ENST00000377770 41.99 17.32 27.81 0.80 1.61 0.90 1.75 0.75 1.27
GALNT5 ENST00000259056 42.00 54.31 46.87 0.80 0.62 0.68 1.75 1.69 1.88
ZDHHC6 ENST00000369405 42.00 42.47 40.48 0.80 0.59 0.80 1.75 1.89 2.04
ZDHHC8 ENST00000405930 42.01 17.60 27.96 0.78 1.57 0.82 1.75 0.73 1.27
CIR1 ENST00000342016 42.01 56.47 48.11 0.78 0.52 0.66 1.75 1.54 1.88
ANGPTL1 ENST00000234816 42.02 70.93 56.24 0.78 0.49 0.49 1.75 1.05 1.76
RBPMS2 ENST00000300069 42.02 20.13 29.23 0.78 1.43 0.84 1.75 0.75 1.34
ZNF668 ENST00000417110 42.03 82.38 63.31 0.78 0.34 0.48 1.75 0.52 1.36
ITGA10 ENST00000369304 42.03 43.21 40.79 0.80 0.62 0.81 1.74 1.92 2.04
E2F2 ENST00000361729 42.04 30.02 34.31 0.80 1.09 0.87 1.74 1.43 1.76
NDRG1 ENST00000414097 42.04 31.28 34.85 0.80 0.99 0.90 1.74 1.38 1.75
CNTNAP5 ENST00000431078 42.05 11.53 24.82 0.78 2.11 1.04 1.74 0.57 1.10
STX4 ENST00000313843 42.05 59.95 49.99 0.78 0.53 0.62 1.74 1.37 1.90
GAS2 ENST00000454584 42.06 43.85 41.15 0.78 0.61 0.75 1.74 1.97 2.02
WDPCP ENST00000272321 42.06 41.61 40.12 0.78 0.62 0.81 1.75 1.81 1.99
ORC2 ENST00000234296 42.07 17.22 27.80 0.78 1.61 0.90 1.75 0.74 1.27
TTPAL ENST00000372904 42.07 37.28 37.95 0.78 0.76 0.85 1.75 1.66 2.02
PACS2 ENST00000458164 42.08 5.72 22.01 0.78 2.92 1.18 1.75 0.34 0.97
DNAJC1 ENST00000376980 42.08 43.74 41.12 0.78 0.62 0.76 1.75 1.95 2.04
RNF25 ENST00000295704 42.09 27.88 33.13 0.78 1.21 0.87 1.75 1.19 1.68
AWAT1 ENST00000374521 42.09 66.94 54.02 0.78 0.53 0.59 1.75 1.25 1.76

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.