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
DYNC2H1 ENST00000398093 48.81 27.82 36.45 0.52 1.23 0.84 1.83 1.18 1.89
PCCA ENST00000376285 48.82 48.28 47.30 0.52 0.63 0.66 1.82 2.00 1.87
NT5DC1 ENST00000319550 48.82 48.83 47.62 0.52 0.63 0.65 1.82 2.02 1.88
YIPF1 ENST00000072644 48.83 40.37 42.93 0.52 0.61 0.67 1.82 1.76 2.00
PFDN5 ENST00000551018 48.84 66.17 57.42 0.52 0.53 0.51 1.82 1.21 1.67
MSH2 ENST00000233146 48.84 14.55 29.87 0.52 2.04 0.86 1.83 0.61 1.44
SGPP1 ENST00000247225 48.85 54.98 50.97 0.52 0.57 0.66 1.83 1.64 1.86
SYT10 ENST00000228567 48.85 40.04 42.79 0.52 0.63 0.70 1.83 1.69 2.02
RANBP17 ENST00000523189 48.86 71.89 60.99 0.52 0.51 0.43 1.83 1.07 1.58
SCPEP1 ENST00000262288 48.86 63.57 55.89 0.52 0.51 0.49 1.83 1.25 1.76
C5orf54 ENST00000408953 48.87 52.50 49.62 0.52 0.66 0.67 1.82 1.83 1.84
MMP15 ENST00000219271 48.87 25.31 35.29 0.52 1.28 0.86 1.82 1.03 1.75
CA3 ENST00000285381 48.88 45.10 45.68 0.52 0.68 0.68 1.82 1.97 1.99
FAM216A ENST00000377673 48.88 41.39 43.54 0.52 0.62 0.62 1.82 1.80 2.00
POLR2K ENST00000353107 48.89 85.28 69.18 0.52 0.25 0.44 1.82 0.46 0.99
VPS13C ENST00000261517 48.89 34.59 40.07 0.53 0.80 0.82 1.82 1.54 1.99
SNURF ENST00000338094 48.90 43.47 44.81 0.53 0.61 0.66 1.82 1.96 2.04
DHX37 ENST00000308736 48.90 11.63 28.44 0.54 2.09 0.78 1.82 0.57 1.30
OVOL2 ENST00000278780 48.91 29.70 37.57 0.54 1.11 0.84 1.82 1.39 2.01
CLN3 ENST00000569430 48.91 50.72 48.71 0.54 0.63 0.68 1.81 1.94 1.85
FABP7 ENST00000368444 48.92 83.41 68.16 0.54 0.27 0.49 1.80 0.47 1.08
CAMLG ENST00000297156 48.92 65.17 56.91 0.54 0.51 0.49 1.80 1.24 1.71
CDH3 ENST00000264012 48.93 46.91 46.61 0.54 0.71 0.66 1.80 1.94 1.89
MRPL22 ENST00000523037 48.93 72.71 61.51 0.54 0.47 0.46 1.80 1.03 1.48
CREB3L2 ENST00000330387 48.94 34.35 39.99 0.54 0.82 0.81 1.80 1.56 1.99

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.