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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
DND1 ENST00000542735 7.11 27.37 15.05 2.88 1.25 1.87 0.38 1.17 0.63
ING1 ENST00000375774 7.11 34.78 18.93 2.88 0.77 1.54 0.38 1.55 0.83
BTG3 ENST00000339775 7.12 17.71 9.96 2.88 1.53 2.28 0.38 0.73 0.42
UPRT ENST00000373383 7.12 28.15 15.44 2.90 1.18 1.82 0.38 1.20 0.67
TRIM46 ENST00000334634 7.13 8.80 5.23 2.90 2.47 3.56 0.38 0.48 0.26
NFKBID ENST00000396901 7.13 27.93 15.33 2.90 1.20 1.80 0.38 1.19 0.66
POLR3B ENST00000228347 7.14 43.56 23.44 2.91 0.61 1.19 0.38 1.96 1.01
HACE1 ENST00000262903 7.14 23.82 13.07 2.90 1.38 2.10 0.38 0.93 0.52
FKBP1A ENST00000400137 7.15 27.31 15.03 2.91 1.25 1.89 0.38 1.15 0.63
DPY30 ENST00000342166 7.15 52.25 27.82 2.91 0.62 0.90 0.38 1.84 1.28
PTPN11 ENST00000351677 7.16 2.26 2.39 2.91 3.64 4.04 0.38 0.30 0.23
CPEB3 ENST00000265997 7.16 4.64 3.35 2.90 3.27 3.90 0.38 0.31 0.23
ESR1 ENST00000440973 7.17 4.84 3.45 2.90 3.28 3.85 0.38 0.31 0.23
TIPRL ENST00000367833 7.17 15.83 8.86 2.90 1.89 2.47 0.38 0.68 0.38
CDC27 ENST00000531206 7.18 9.02 5.41 2.90 2.43 3.48 0.38 0.47 0.25
GRIN2D ENST00000263269 7.18 3.75 2.88 2.91 3.33 4.02 0.38 0.31 0.23
RBM8A ENST00000330165 7.19 27.89 15.31 2.91 1.21 1.81 0.38 1.19 0.66
NFKB2 ENST00000369966 7.19 3.87 2.94 2.91 3.30 4.00 0.38 0.31 0.23
DR1 ENST00000370272 7.20 16.43 9.25 2.91 1.80 2.30 0.38 0.69 0.38
RAF1 ENST00000251849 7.21 15.38 8.64 2.91 1.90 2.54 0.38 0.68 0.36
RCC2 ENST00000375436 7.21 14.47 8.20 2.91 2.04 2.57 0.38 0.61 0.37
NEGR1 ENST00000357731 7.22 10.94 6.40 2.91 2.10 3.06 0.38 0.51 0.32
GPATCH8 ENST00000591680 7.22 4.31 3.21 2.91 3.25 3.90 0.38 0.32 0.24
NAMPT ENST00000222553 7.23 12.77 7.38 2.91 2.09 2.80 0.38 0.59 0.34
ARL8B ENST00000256496 7.23 35.38 19.33 2.91 0.77 1.53 0.38 1.56 0.85

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