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
ZNF552 ENST00000391701 95.04 94.12 97.27 0.10 0.25 0.08 0.12 0.25 0.07
ZNF880 ENST00000422689 95.05 86.31 93.42 0.10 0.25 0.11 0.12 0.43 0.15
C12orf36 ENST00000318426 95.05 89.86 95.21 0.10 0.27 0.08 0.12 0.37 0.10
OR1M1 ENST00000429566 95.06 97.71 98.61 0.10 0.21 0.10 0.12 0.18 0.05
LPAR5 ENST00000329858 95.06 59.45 80.58 0.10 0.51 0.39 0.12 1.41 0.52
SPATA33 ENST00000301031 95.07 95.71 97.90 0.10 0.23 0.09 0.12 0.20 0.04
PRAMEF18 ENST00000376126 95.07 92.72 96.67 0.10 0.29 0.08 0.12 0.30 0.08
ZNF138 ENST00000440155 95.08 86.87 93.77 0.10 0.22 0.10 0.12 0.41 0.13
C6orf48 ENST00000375640 95.08 93.76 97.15 0.10 0.27 0.08 0.12 0.26 0.07
TBC1D26 ENST00000437605 95.09 59.62 80.66 0.10 0.52 0.39 0.12 1.41 0.51
PRR25 ENST00000301698 95.09 95.92 97.99 0.10 0.22 0.09 0.12 0.20 0.04
C11orf40 ENST00000307616 95.10 94.41 97.37 0.10 0.23 0.08 0.12 0.24 0.07
ZNF813 ENST00000396403 95.10 47.67 74.24 0.10 0.61 0.39 0.12 1.97 0.69
ZNF540 ENST00000592533 95.11 52.17 76.75 0.10 0.62 0.34 0.12 1.84 0.61
ZNF233 ENST00000391958 95.11 83.57 92.05 0.10 0.27 0.14 0.12 0.47 0.16
APOC4 ENST00000419266 95.12 92.98 96.86 0.10 0.28 0.08 0.12 0.30 0.07
C8orf49 ENST00000525043 95.12 98.49 98.93 0.10 0.21 0.10 0.12 0.15 0.04
PSG9 ENST00000270077 95.13 91.80 96.19 0.10 0.23 0.07 0.12 0.32 0.10
KIR3DL2 ENST00000326321 95.13 92.20 96.40 0.10 0.25 0.07 0.12 0.31 0.09
SP140 ENST00000392045 95.14 31.10 64.39 0.10 1.02 0.51 0.12 1.36 1.34
GAGE12J ENST00000442437 95.14 95.30 97.79 0.10 0.23 0.09 0.12 0.21 0.04
C22orf39 ENST00000399562 95.15 88.63 94.61 0.10 0.24 0.09 0.12 0.35 0.11
DEFB131 ENST00000334879 95.16 96.40 98.15 0.10 0.22 0.09 0.12 0.19 0.05
GAGE1 ENST00000381700 95.16 96.31 98.15 0.10 0.22 0.09 0.12 0.19 0.05
QRICH2 ENST00000262765 95.17 51.68 76.51 0.10 0.61 0.38 0.12 1.87 0.61

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.