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
FAM209B ENST00000371325 86.78 94.34 93.27 0.24 0.24 0.14 0.40 0.24 0.15
SLX4 ENST00000294008 86.78 44.20 67.28 0.24 0.62 0.52 0.40 1.95 1.15
UBE2U ENST00000371076 86.79 72.39 82.93 0.24 0.51 0.32 0.40 1.03 0.40
TPTE2 ENST00000400230 86.79 48.47 69.86 0.24 0.63 0.46 0.40 2.02 0.92
ZNF596 ENST00000398612 86.80 79.26 86.26 0.24 0.38 0.33 0.40 0.67 0.33
CTRB2 ENST00000303037 86.80 80.85 87.03 0.25 0.35 0.28 0.40 0.57 0.30
OR5H2 ENST00000355273 86.81 92.16 92.14 0.25 0.25 0.14 0.40 0.32 0.16
POLRMT ENST00000588649 86.81 49.19 70.25 0.24 0.66 0.43 0.40 2.04 0.91
BIRC7 ENST00000217169 86.82 71.60 82.62 0.24 0.53 0.32 0.40 1.07 0.43
PYY ENST00000360085 86.82 86.98 89.99 0.24 0.22 0.18 0.40 0.40 0.22
OR4C6 ENST00000314259 86.83 93.80 93.06 0.24 0.27 0.14 0.40 0.26 0.15
HRCT1 ENST00000354323 86.83 99.74 94.93 0.24 0.17 0.09 0.40 0.11 0.11
RNPC3 ENST00000533099 86.84 37.10 63.03 0.24 0.78 0.51 0.40 1.66 1.39
SIRPG ENST00000303415 86.84 88.23 90.62 0.24 0.23 0.15 0.40 0.37 0.20
BSG ENST00000333511 86.85 48.96 70.15 0.24 0.65 0.44 0.40 2.04 0.90
REG3A ENST00000393878 86.86 69.21 81.41 0.24 0.56 0.37 0.40 1.13 0.48
F2RL3 ENST00000248076 86.86 75.94 84.75 0.24 0.43 0.34 0.40 0.86 0.40
FBXO27 ENST00000292853 86.87 89.48 91.12 0.24 0.27 0.15 0.40 0.36 0.19
SSX4B ENST00000376884 86.87 87.52 90.23 0.24 0.23 0.16 0.40 0.38 0.22
IFLTD1 ENST00000458174 86.88 66.28 79.90 0.24 0.54 0.37 0.40 1.20 0.52
RP11-268J15.5 ENST00000373137 86.88 99.80 96.11 0.24 0.17 0.07 0.40 0.11 0.10
NXF2B ENST00000457521 86.89 30.73 58.92 0.24 1.05 0.49 0.39 1.36 1.65
CCL4L2 ENST00000394465 86.89 88.41 90.72 0.24 0.23 0.15 0.39 0.37 0.20
OR2M7 ENST00000317965 86.90 98.70 95.67 0.24 0.18 0.07 0.39 0.15 0.11
ARSD ENST00000381154 86.90 51.10 71.53 0.24 0.66 0.44 0.39 1.92 0.84

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.