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
APOF ENST00000398189 59.79 58.08 59.10 0.59 0.53 0.49 1.39 1.46 1.68
ROBO4 ENST00000306534 59.80 49.16 53.94 0.59 0.66 0.61 1.39 2.04 1.77
SLC45A2 ENST00000296589 59.80 54.40 56.93 0.59 0.62 0.49 1.39 1.66 1.71
LAMP2 ENST00000434600 59.81 32.22 44.58 0.59 0.86 0.62 1.39 1.46 2.05
EGFLAM ENST00000354891 59.81 50.10 54.51 0.59 0.67 0.57 1.39 1.98 1.75
PSKH2 ENST00000276616 59.82 85.53 75.65 0.59 0.27 0.38 1.39 0.44 0.64
THSD4 ENST00000355327 59.82 29.47 43.01 0.59 1.09 0.67 1.39 1.39 2.01
NMBR ENST00000258042 59.83 89.44 77.83 0.59 0.27 0.38 1.39 0.37 0.54
FAM222A ENST00000538780 59.83 21.50 38.98 0.59 1.42 0.80 1.39 0.79 2.07
ACRBP ENST00000229243 59.84 51.70 55.43 0.59 0.61 0.49 1.39 1.88 1.72
PRIMPOL ENST00000314970 59.84 72.02 67.83 0.59 0.52 0.51 1.39 1.04 1.12
DCDC1 ENST00000452803 59.85 69.54 66.38 0.59 0.54 0.53 1.39 1.11 1.20
UBXN2B ENST00000399598 59.85 35.82 46.50 0.59 0.80 0.66 1.39 1.58 1.91
LETM2 ENST00000523983 59.86 77.12 70.83 0.61 0.42 0.43 1.38 0.78 0.86
ALDH8A1 ENST00000265605 59.86 77.27 70.96 0.62 0.42 0.43 1.38 0.77 0.85
NOLC1 ENST00000605788 59.87 31.57 44.17 0.63 0.94 0.61 1.37 1.44 2.05
DCPS ENST00000263579 59.87 70.04 66.66 0.63 0.53 0.53 1.37 1.14 1.20
SIAH3 ENST00000400405 59.88 81.39 73.44 0.63 0.33 0.42 1.37 0.54 0.76
GPR115 ENST00000283303 59.88 67.30 65.04 0.63 0.56 0.51 1.37 1.21 1.31
NARG2 ENST00000261520 59.89 45.12 51.66 0.63 0.70 0.62 1.37 1.96 1.93
CEP290 ENST00000552810 59.89 51.69 55.45 0.63 0.61 0.51 1.37 1.87 1.73
SOX12 ENST00000342665 59.90 23.83 40.14 0.63 1.38 0.82 1.38 0.93 1.99
ACTRT3 ENST00000330368 59.90 85.54 75.72 0.63 0.27 0.38 1.38 0.44 0.64
OMA1 ENST00000371226 59.91 61.26 61.25 0.63 0.53 0.43 1.39 1.40 1.48
NCAPH2 ENST00000299821 59.91 29.90 43.26 0.63 1.13 0.65 1.39 1.41 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.