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
RXFP1 ENST00000307765 34.09 46.76 38.68 0.95 0.72 0.82 1.77 1.97 2.02
CHCHD1 ENST00000372833 34.10 92.99 64.99 0.95 0.28 0.51 1.77 0.30 1.31
GRB14 ENST00000263915 34.10 22.82 26.61 0.95 1.44 0.97 1.77 0.88 1.25
LRRC59 ENST00000225972 34.11 29.11 29.78 0.95 1.14 0.86 1.76 1.33 1.43
CCDC71 ENST00000321895 34.11 47.75 39.31 0.95 0.59 0.80 1.76 1.99 2.04
PDE3B ENST00000282096 34.12 25.44 27.92 0.95 1.25 0.85 1.76 1.05 1.29
SPIN2B ENST00000333933 34.13 84.70 59.73 0.95 0.27 0.49 1.75 0.42 1.66
CRBN ENST00000231948 34.13 34.16 32.36 0.95 0.84 0.91 1.76 1.55 1.61
INTS9 ENST00000521022 34.14 39.88 35.20 0.95 0.63 0.86 1.77 1.70 1.75
DARS ENST00000264161 34.14 36.25 33.35 0.95 0.82 0.87 1.77 1.61 1.72
HIST1H3I ENST00000328488 34.15 88.80 62.30 0.95 0.25 0.49 1.77 0.35 1.42
PI4K2B ENST00000264864 34.15 50.65 40.59 0.95 0.63 0.81 1.77 1.95 2.04
SAE1 ENST00000270225 34.16 9.98 20.13 0.95 2.33 1.49 1.77 0.49 0.86
RPN1 ENST00000296255 34.16 23.90 27.18 0.95 1.39 0.99 1.77 0.95 1.25
SH2D3C ENST00000314830 34.17 29.74 30.14 0.95 1.11 0.81 1.77 1.40 1.46
EXOC3 ENST00000512944 34.17 15.50 23.00 0.95 1.87 1.20 1.78 0.67 0.98
PTGR2 ENST00000555661 34.18 59.50 45.56 0.95 0.51 0.70 1.78 1.41 1.97
EXOC4 ENST00000253861 34.18 41.98 36.22 0.95 0.61 0.87 1.78 1.83 1.83
RPS6KC1 ENST00000366960 34.19 23.71 27.10 0.95 1.39 0.99 1.78 0.93 1.26
REXO2 ENST00000265881 34.19 37.84 34.29 0.95 0.80 0.87 1.78 1.70 1.76
ECEL1 ENST00000304546 34.20 46.81 38.78 0.95 0.72 0.82 1.78 1.97 2.03
SELENBP1 ENST00000368868 34.20 74.91 54.06 0.95 0.53 0.59 1.78 0.94 1.77
TAB3 ENST00000378933 34.21 20.62 25.48 0.95 1.46 1.02 1.78 0.77 1.19
MITD1 ENST00000289359 34.21 58.66 45.11 0.95 0.54 0.70 1.78 1.43 2.01
TDRD7 ENST00000355295 34.22 19.86 25.12 0.95 1.42 1.05 1.78 0.74 1.16

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.