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
GM2A ENST00000357164 78.38 69.33 77.01 0.35 0.56 0.37 0.66 1.14 0.61
TVP23A ENST00000299866 78.39 65.35 74.75 0.34 0.52 0.40 0.66 1.25 0.66
IL26 ENST00000229134 78.39 74.54 79.79 0.34 0.53 0.38 0.66 1.00 0.53
KNCN ENST00000396314 78.40 96.65 90.60 0.34 0.23 0.15 0.66 0.20 0.20
IL4I1 ENST00000595948 78.41 49.03 65.18 0.34 0.66 0.52 0.66 2.03 1.30
MIS18A ENST00000290130 78.41 54.43 68.42 0.34 0.61 0.47 0.66 1.66 1.06
MRPL38 ENST00000309352 78.42 60.52 72.08 0.34 0.52 0.43 0.66 1.41 0.81
BGLAP ENST00000368272 78.42 96.89 90.73 0.34 0.23 0.15 0.66 0.19 0.20
CDRT1 ENST00000395906 78.43 55.20 68.82 0.34 0.57 0.46 0.66 1.62 1.05
OTOP1 ENST00000296358 78.43 91.34 88.05 0.34 0.23 0.23 0.66 0.34 0.31
CYP2C18 ENST00000285979 78.44 72.14 78.52 0.34 0.52 0.38 0.66 1.04 0.55
MYADML2 ENST00000409745 78.44 88.13 86.46 0.34 0.24 0.30 0.66 0.38 0.33
FGFR1OP ENST00000366847 78.45 35.47 56.80 0.34 0.77 0.52 0.66 1.56 1.71
DNASE1L2 ENST00000564065 78.45 75.94 80.53 0.34 0.43 0.39 0.66 0.86 0.51
WDFY4 ENST00000325239 78.46 12.22 43.68 0.34 2.06 0.61 0.66 0.58 2.01
RASSF6 ENST00000342081 78.46 95.35 90.00 0.34 0.24 0.18 0.66 0.21 0.22
ORAOV1 ENST00000279147 78.47 73.88 79.43 0.34 0.53 0.39 0.66 1.03 0.52
HAUS6 ENST00000380502 78.47 53.19 67.69 0.34 0.66 0.52 0.66 1.75 1.12
SLC18A1 ENST00000440926 78.48 84.15 84.65 0.34 0.27 0.34 0.66 0.45 0.40
OR10J1 ENST00000423932 78.48 94.96 89.80 0.34 0.23 0.18 0.66 0.21 0.23
PROZ ENST00000342783 78.49 86.35 85.73 0.34 0.25 0.33 0.66 0.43 0.33
OR52A5 ENST00000307388 78.49 89.65 87.26 0.34 0.27 0.28 0.66 0.36 0.31
LRRN4CL ENST00000317449 78.50 95.28 89.97 0.34 0.23 0.18 0.66 0.21 0.23
LPPR3 ENST00000359894 78.50 40.51 59.94 0.34 0.63 0.49 0.66 1.77 1.63
NDUFB10 ENST00000268668 78.51 59.26 71.40 0.34 0.49 0.44 0.66 1.43 0.87

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.