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
OR1G1 ENST00000328890 80.84 89.46 88.33 0.32 0.27 0.22 0.60 0.36 0.30
RBM44 ENST00000316997 80.84 25.78 52.62 0.32 1.23 0.61 0.60 1.05 1.89
HLA-A ENST00000396634 80.85 37.11 59.17 0.32 0.78 0.49 0.60 1.66 1.68
TMPRSS9 ENST00000332578 80.85 51.61 68.23 0.32 0.62 0.52 0.60 1.88 1.08
C11orf94 ENST00000449465 80.86 89.09 88.12 0.32 0.27 0.23 0.60 0.35 0.30
MMP26 ENST00000380390 80.86 86.21 86.71 0.32 0.27 0.30 0.61 0.42 0.32
C1orf105 ENST00000367727 80.87 83.50 85.54 0.32 0.27 0.33 0.61 0.46 0.35
MAGEF1 ENST00000317897 80.87 86.05 86.65 0.32 0.27 0.30 0.61 0.43 0.33
FAM169B ENST00000558256 80.88 66.72 76.93 0.32 0.56 0.35 0.61 1.21 0.60
CCDC102B ENST00000360242 80.88 68.92 78.08 0.32 0.54 0.39 0.61 1.16 0.55
TMEM190 ENST00000291934 80.89 83.13 85.34 0.32 0.29 0.34 0.60 0.49 0.36
DNAJC4 ENST00000321685 80.89 86.54 86.91 0.32 0.24 0.29 0.60 0.42 0.31
MTUS1 ENST00000262102 80.90 38.42 60.08 0.32 0.75 0.47 0.60 1.70 1.61
PABPN1L ENST00000419291 80.90 92.55 89.83 0.32 0.29 0.18 0.60 0.31 0.23
MMP25 ENST00000336577 80.91 68.00 77.65 0.32 0.52 0.38 0.60 1.19 0.55
COQ4 ENST00000300452 80.92 75.55 81.61 0.32 0.44 0.37 0.60 0.90 0.47
CARD14 ENST00000573882 80.92 52.98 69.02 0.32 0.66 0.46 0.60 1.78 1.03
OR2G2 ENST00000320065 80.93 74.44 81.03 0.32 0.53 0.39 0.60 1.00 0.50
LAT2 ENST00000460943 80.93 45.65 64.64 0.32 0.73 0.51 0.60 2.01 1.32
TMEM186 ENST00000333050 80.94 81.20 84.38 0.32 0.35 0.33 0.60 0.54 0.40
ZNF333 ENST00000292530 80.94 66.32 76.73 0.32 0.54 0.34 0.60 1.20 0.60
CNTD2 ENST00000430325 80.95 75.89 81.80 0.32 0.43 0.37 0.60 0.88 0.46
OSCAR ENST00000359649 80.95 80.53 84.02 0.32 0.37 0.35 0.60 0.59 0.42
GPR160 ENST00000355897 80.96 68.88 78.17 0.32 0.54 0.39 0.60 1.18 0.55
PCED1B ENST00000546455 80.96 98.74 93.10 0.32 0.16 0.14 0.60 0.15 0.15

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.