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
STAC2 ENST00000333461 63.79 52.37 58.14 0.59 0.62 0.48 1.22 1.82 1.65
TMEM199 ENST00000292114 63.80 77.95 73.66 0.59 0.42 0.40 1.22 0.79 0.73
OR52N1 ENST00000317078 63.80 65.46 66.33 0.59 0.54 0.53 1.22 1.25 1.20
PALD1 ENST00000263563 63.81 46.27 54.61 0.59 0.73 0.56 1.22 2.04 1.74
ACAN ENST00000439576 63.81 4.75 32.48 0.59 3.27 0.89 1.22 0.32 1.63
TINAG ENST00000259782 63.82 75.45 72.32 0.59 0.46 0.44 1.22 0.90 0.82
OR8D2 ENST00000357438 63.82 79.80 74.71 0.59 0.35 0.40 1.22 0.62 0.67
A4GNT ENST00000236709 63.83 39.00 50.44 0.59 0.70 0.67 1.22 1.64 1.89
TMEM79 ENST00000405535 63.83 65.75 66.47 0.59 0.54 0.51 1.22 1.22 1.22
PURB ENST00000395699 63.84 32.97 47.13 0.59 0.84 0.67 1.22 1.48 1.89
COMMD5 ENST00000450361 63.84 93.68 82.14 0.59 0.28 0.35 1.22 0.27 0.45
TXNRD1 ENST00000525566 63.85 37.00 49.31 0.59 0.77 0.70 1.22 1.68 1.85
B4GALT7 ENST00000029410 63.86 64.56 65.82 0.58 0.48 0.51 1.22 1.21 1.25
SERPINB1 ENST00000380739 63.86 79.13 74.38 0.58 0.39 0.40 1.22 0.69 0.70
OPN4 ENST00000372071 63.87 73.54 71.18 0.58 0.53 0.44 1.22 1.03 0.86
FAM83D ENST00000217429 63.87 68.62 68.24 0.58 0.53 0.52 1.22 1.18 1.08
TRPM4 ENST00000252826 63.88 60.50 63.30 0.58 0.52 0.49 1.22 1.41 1.36
OR11H6 ENST00000315519 63.88 81.32 75.57 0.58 0.33 0.38 1.22 0.54 0.64
RPL7L1 ENST00000493763 63.89 46.90 54.98 0.58 0.71 0.52 1.22 1.94 1.74
ATP6AP1L ENST00000380167 63.89 53.37 58.73 0.58 0.66 0.52 1.22 1.70 1.65
OR2H2 ENST00000383640 63.90 89.45 80.00 0.58 0.27 0.35 1.22 0.36 0.52
GCAT ENST00000323205 63.90 68.56 68.22 0.58 0.53 0.52 1.21 1.19 1.08
HTR3A ENST00000355556 63.91 65.05 66.14 0.58 0.51 0.52 1.21 1.24 1.20
DFFA ENST00000377038 63.91 65.66 66.45 0.58 0.53 0.51 1.21 1.22 1.22
PAQR4 ENST00000318782 63.92 87.74 79.16 0.58 0.24 0.38 1.21 0.37 0.54

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.