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
CCDC178 ENST00000383096 83.42 61.76 75.54 0.30 0.57 0.37 0.51 1.37 0.65
C2orf71 ENST00000331664 83.43 62.70 76.09 0.30 0.51 0.38 0.51 1.31 0.62
ATP5J ENST00000457143 83.43 77.02 83.61 0.30 0.43 0.33 0.51 0.78 0.40
ZNF619 ENST00000447116 83.44 54.43 71.44 0.30 0.62 0.46 0.51 1.66 0.86
LYPD4 ENST00000330743 83.44 84.78 87.30 0.30 0.27 0.28 0.51 0.42 0.31
KRTAP4-4 ENST00000390661 83.45 91.48 90.53 0.30 0.23 0.15 0.51 0.32 0.21
TTC16 ENST00000373289 83.45 59.11 74.12 0.30 0.49 0.39 0.51 1.44 0.69
ZNF132 ENST00000254166 83.46 71.93 81.05 0.30 0.51 0.39 0.51 1.07 0.49
FAM129C ENST00000335393 83.46 59.82 74.57 0.30 0.52 0.40 0.51 1.37 0.68
RECQL4 ENST00000428558 83.47 64.50 77.13 0.30 0.48 0.37 0.51 1.22 0.59
FAM150A ENST00000358543 83.47 91.64 90.64 0.30 0.24 0.15 0.52 0.32 0.20
PLEKHD1 ENST00000322564 83.48 39.89 62.59 0.30 0.63 0.48 0.52 1.70 1.40
CRIP2 ENST00000483017 83.48 51.26 69.56 0.30 0.65 0.44 0.52 1.90 0.96
GPRIN1 ENST00000303991 83.49 13.72 47.36 0.30 2.06 0.66 0.52 0.60 1.85
CYP2W1 ENST00000308919 83.49 60.90 75.14 0.30 0.56 0.39 0.52 1.41 0.67
ZIM2 ENST00000391708 83.50 40.77 63.23 0.30 0.62 0.49 0.52 1.78 1.36
HIST1H3A ENST00000357647 83.50 97.32 93.16 0.30 0.23 0.14 0.52 0.19 0.15
AGAP6 ENST00000412531 83.51 81.18 85.66 0.30 0.35 0.33 0.52 0.55 0.34
PXT1 ENST00000454782 83.51 95.21 92.06 0.30 0.23 0.14 0.52 0.21 0.16
C12orf77 ENST00000549828 83.52 83.27 86.59 0.30 0.28 0.30 0.52 0.47 0.33
CCDC64B ENST00000572449 83.52 56.67 72.82 0.30 0.53 0.43 0.52 1.55 0.81
KLK14 ENST00000391802 83.53 80.52 85.40 0.30 0.37 0.34 0.52 0.59 0.35
HCST ENST00000246551 83.53 88.32 89.06 0.30 0.23 0.19 0.52 0.37 0.26
TFDP3 ENST00000310125 83.54 98.61 93.98 0.30 0.20 0.09 0.52 0.15 0.11
KRTAP20-1 ENST00000334664 83.54 98.02 93.61 0.30 0.20 0.13 0.52 0.16 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.