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
PMEPA1 ENST00000341744 59.02 15.24 35.35 0.56 1.90 0.87 1.49 0.67 1.77
TMEM132D ENST00000422113 59.02 5.44 30.39 0.56 3.02 0.81 1.48 0.33 1.46
KRT35 ENST00000393989 59.03 48.21 53.01 0.56 0.63 0.61 1.48 1.99 1.87
DZIP1L ENST00000327532 59.03 70.90 66.64 0.56 0.49 0.52 1.48 1.07 1.20
SLC1A1 ENST00000262352 59.04 44.21 50.68 0.56 0.62 0.66 1.48 1.95 1.85
SARDH ENST00000371872 59.04 46.49 51.95 0.56 0.73 0.62 1.48 2.02 1.92
LRRC15 ENST00000439944 59.05 75.86 69.67 0.56 0.43 0.44 1.48 0.88 0.95
TTF2 ENST00000369466 59.05 47.97 52.82 0.56 0.61 0.61 1.48 1.99 1.88
MEP1A ENST00000230588 59.06 51.07 54.62 0.56 0.65 0.56 1.48 1.92 1.73
TSKS ENST00000246801 59.06 9.87 32.66 0.56 2.37 0.86 1.48 0.50 1.63
CYP11A1 ENST00000268053 59.07 49.63 53.78 0.56 0.66 0.62 1.48 2.02 1.80
PPCDC ENST00000342932 59.07 78.33 71.16 0.56 0.43 0.44 1.48 0.74 0.86
C1orf189 ENST00000368525 59.08 94.45 80.09 0.56 0.23 0.35 1.48 0.24 0.52
CYSLTR1 ENST00000373304 59.08 85.93 75.45 0.56 0.28 0.38 1.48 0.43 0.66
GNRH1 ENST00000276414 59.09 55.73 57.30 0.56 0.52 0.51 1.48 1.60 1.68
CHID1 ENST00000454838 59.09 40.26 48.55 0.56 0.61 0.68 1.47 1.73 1.85
LYPD5 ENST00000377950 59.10 75.45 69.41 0.56 0.46 0.43 1.47 0.90 0.98
CORIN ENST00000273857 59.10 65.77 63.64 0.56 0.54 0.49 1.48 1.22 1.38
MFNG ENST00000356998 59.11 79.36 71.79 0.56 0.38 0.46 1.48 0.67 0.81
OR51L1 ENST00000321543 59.11 81.83 73.22 0.56 0.35 0.43 1.48 0.51 0.79
COL19A1 ENST00000322773 59.12 50.68 54.46 0.56 0.63 0.57 1.48 1.95 1.76
SLC25A45 ENST00000398802 59.12 76.35 69.97 0.54 0.43 0.47 1.48 0.85 0.92
FANK1 ENST00000368693 59.13 65.70 63.59 0.54 0.53 0.49 1.48 1.22 1.40
ATP7B ENST00000242839 59.13 65.59 63.55 0.54 0.53 0.49 1.47 1.22 1.39
C5orf48 ENST00000357147 59.14 85.82 75.40 0.53 0.28 0.37 1.47 0.44 0.65

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.