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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
CDK6 ENST00000265734 3.10 10.90 4.27 3.87 2.11 3.75 0.30 0.50 0.24
CTNNB1 ENST00000349496 3.11 2.09 0.93 3.87 3.69 4.46 0.30 0.28 0.21
QKI ENST00000361752 3.11 20.95 9.51 3.87 1.43 2.30 0.30 0.83 0.40
ACVR2A ENST00000241416 3.12 3.82 1.47 3.87 3.31 4.34 0.30 0.31 0.22
PCMT1 ENST00000367384 3.12 22.02 10.12 3.86 1.48 2.24 0.30 0.81 0.42
XPO7 ENST00000252512 3.13 1.93 0.87 3.86 3.75 4.50 0.30 0.26 0.20
PLCB1 ENST00000338037 3.14 12.54 5.09 3.86 2.09 3.64 0.30 0.58 0.25
MARCH5 ENST00000358935 3.14 17.72 7.78 3.86 1.53 2.64 0.30 0.72 0.33
PRPF4B ENST00000337659 3.15 1.73 0.82 3.85 3.84 4.54 0.30 0.26 0.21
THOC1 ENST00000261600 3.15 8.00 3.00 3.85 2.56 3.97 0.30 0.44 0.24
PPP1R9B ENST00000316878 3.16 4.18 1.62 3.85 3.25 4.28 0.30 0.32 0.23
XPR1 ENST00000367590 3.16 3.40 1.32 3.86 3.42 4.34 0.30 0.29 0.22
TRAF6 ENST00000526995 3.17 7.08 2.62 3.86 2.57 4.00 0.30 0.37 0.23
SOX5 ENST00000451604 3.17 4.77 1.82 3.86 3.27 4.21 0.30 0.32 0.23
RPL30 ENST00000521291 3.18 23.56 11.01 3.87 1.39 2.20 0.30 0.93 0.44
ABHD17B ENST00000377041 3.18 27.17 12.74 3.87 1.24 2.16 0.30 1.14 0.52
USP47 ENST00000339865 3.19 2.11 0.94 3.88 3.68 4.45 0.30 0.28 0.21
CCDC101 ENST00000317058 3.19 44.28 21.86 3.88 0.61 1.21 0.30 1.96 0.95
MTF2 ENST00000370298 3.20 5.66 2.13 3.88 2.96 4.08 0.30 0.33 0.23
SF3B3 ENST00000302516 3.20 4.44 1.72 3.87 3.27 4.24 0.30 0.32 0.23
RSBN1 ENST00000261441 3.21 20.93 9.53 3.87 1.43 2.29 0.30 0.83 0.40
CLCN3 ENST00000347613 3.21 7.10 2.64 3.87 2.58 4.01 0.30 0.37 0.23
MATR3 ENST00000394805 3.22 0.53 0.54 3.87 4.14 4.71 0.30 0.27 0.17
HNRNPR ENST00000374616 3.22 3.51 1.39 3.86 3.38 4.36 0.30 0.29 0.23
HOMER1 ENST00000334082 3.23 2.60 1.09 3.86 3.55 4.43 0.30 0.29 0.21

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