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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
GREM2 ENST00000318160 31.90 68.32 48.99 0.95 0.52 0.72 1.72 1.20 1.84
C19orf10 ENST00000262947 31.90 80.40 55.82 0.95 0.37 0.52 1.73 0.59 1.75
RNF181 ENST00000306368 31.91 87.78 60.31 0.95 0.24 0.47 1.73 0.37 1.60
HBE1 ENST00000380237 31.91 79.85 55.57 0.95 0.35 0.52 1.73 0.61 1.73
DAB2 ENST00000320816 31.92 19.98 24.00 0.96 1.46 1.10 1.73 0.73 1.05
TMOD4 ENST00000295314 31.93 59.01 43.83 0.96 0.51 0.61 1.73 1.43 2.02
ALG8 ENST00000299626 31.93 43.01 35.62 0.96 0.61 0.86 1.73 1.89 1.77
ST8SIA5 ENST00000315087 31.94 45.13 36.70 0.96 0.70 0.82 1.73 1.96 1.93
SEMA6C ENST00000368913 31.94 34.10 31.24 0.96 0.84 0.86 1.73 1.53 1.56
E2F7 ENST00000322886 31.95 11.69 19.86 0.96 2.10 1.47 1.72 0.57 0.85
ARHGAP19 ENST00000358531 31.95 57.71 43.20 0.96 0.57 0.65 1.72 1.48 1.99
SLC38A5 ENST00000376876 31.96 12.58 20.35 0.96 2.10 1.49 1.72 0.58 0.88
LHCGR ENST00000294954 31.96 46.77 37.62 0.96 0.72 0.82 1.72 1.97 2.01
PCMTD2 ENST00000308824 31.97 41.14 34.77 0.96 0.59 0.90 1.72 1.82 1.75
PPAP2A ENST00000264775 31.97 39.99 34.25 0.96 0.63 0.87 1.72 1.69 1.76
TRPM6 ENST00000360774 31.98 21.18 24.64 0.96 1.44 1.06 1.72 0.81 1.10
TMA7 ENST00000438607 31.98 87.17 60.00 0.96 0.20 0.48 1.72 0.41 1.63
NFXL1 ENST00000507489 31.99 24.28 26.28 0.96 1.30 1.01 1.72 0.98 1.26
NAP1L5 ENST00000323061 31.99 39.69 34.04 0.95 0.66 0.90 1.72 1.66 1.73
CHRNA1 ENST00000261007 32.00 57.63 43.18 0.95 0.56 0.65 1.72 1.48 1.99
TMEM245 ENST00000374586 32.00 30.15 29.22 0.96 1.09 0.82 1.72 1.40 1.33
SUPV3L1 ENST00000359655 32.01 23.37 25.80 0.96 1.40 1.01 1.71 0.93 1.23
RNF128 ENST00000255499 32.01 36.78 32.62 0.96 0.76 0.87 1.71 1.65 1.63
FLT3 ENST00000241453 32.02 15.45 21.87 0.96 1.87 1.21 1.71 0.67 0.95
C2orf69 ENST00000319974 32.02 42.47 35.45 0.96 0.59 0.87 1.71 1.88 1.77

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