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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
CTNND2 ENST00000304623 16.51 1.04 6.03 1.44 4.05 3.29 0.81 0.28 0.30
ZNF521 ENST00000361524 8.81 1.04 2.52 2.42 4.06 4.01 0.45 0.28 0.24
ACTN4 ENST00000252699 6.48 1.05 1.66 3.04 4.06 4.26 0.37 0.28 0.23
WHSC1 ENST00000382895 1.78 1.05 0.32 4.27 4.06 4.83 0.22 0.28 0.18
COL3A1 ENST00000304636 11.52 1.06 3.67 1.72 4.05 3.82 0.59 0.28 0.23
CREBRF ENST00000296953 2.11 1.06 0.40 4.20 4.05 4.78 0.25 0.28 0.18
CCT3 ENST00000295688 20.49 1.07 8.15 1.53 4.05 2.59 1.02 0.28 0.37
SON ENST00000356577 8.24 1.07 2.34 2.54 4.04 4.03 0.43 0.28 0.23
UPF2 ENST00000356352 11.79 1.08 3.79 1.67 4.04 3.79 0.59 0.28 0.24
PLEKHA5 ENST00000429027 16.41 1.08 6.01 1.48 4.04 3.28 0.81 0.28 0.30
SCAF8 ENST00000367178 15.72 1.09 5.67 1.57 4.03 3.35 0.77 0.28 0.27
ARID2 ENST00000334344 6.85 1.09 1.83 2.92 4.03 4.21 0.37 0.28 0.24
SP1 ENST00000327443 24.89 1.10 10.59 1.37 4.03 2.16 1.13 0.28 0.44
GATAD2B ENST00000368655 6.88 1.11 1.85 2.92 4.02 4.20 0.36 0.28 0.24
TAB2 ENST00000367456 10.38 1.11 3.18 2.04 4.02 3.90 0.54 0.28 0.24
ARCN1 ENST00000264028 16.99 1.12 6.37 1.46 4.02 3.07 0.86 0.28 0.32
PPP3CB ENST00000394829 1.92 1.12 0.38 4.28 4.01 4.78 0.24 0.28 0.18
ILF3 ENST00000449870 8.71 1.13 2.51 2.42 4.01 4.01 0.44 0.28 0.24
MAPK8IP2 ENST00000329492 38.03 1.13 17.45 0.91 4.01 1.62 1.73 0.28 0.76
CARM1 ENST00000327064 2.47 1.14 0.51 4.10 4.00 4.71 0.27 0.28 0.17
RPTOR ENST00000306801 5.88 1.14 1.52 3.15 4.00 4.33 0.33 0.28 0.22
PAXIP1 ENST00000404141 24.78 1.15 10.55 1.39 4.00 2.18 1.12 0.28 0.43
BTK ENST00000308731 4.40 1.15 1.03 3.72 3.99 4.45 0.30 0.28 0.21
PSMD2 ENST00000310118 9.17 1.16 2.65 2.28 4.01 4.00 0.47 0.28 0.23
RFX7 ENST00000423270 19.35 1.16 7.61 1.56 4.01 2.73 0.96 0.28 0.33

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