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
CPSF3 ENST00000238112 4.78 36.86 18.83 3.61 0.76 1.56 0.30 1.68 0.83
TIMP3 ENST00000266085 4.79 26.56 13.29 3.61 1.19 2.06 0.30 1.12 0.54
FGF12 ENST00000454309 4.79 27.17 13.63 3.61 1.24 2.00 0.30 1.14 0.57
ZBTB1 ENST00000394712 4.80 10.24 4.78 3.60 2.29 3.67 0.30 0.49 0.25
FAM49A ENST00000381323 4.80 26.64 13.33 3.60 1.19 2.05 0.30 1.12 0.55
HNRNPL ENST00000221419 4.81 9.33 4.34 3.60 2.48 3.74 0.30 0.49 0.24
HUWE1 ENST00000342160 4.81 0.25 0.86 3.60 4.12 4.51 0.30 0.28 0.20
PELP1 ENST00000574876 4.82 3.36 1.91 3.61 3.44 4.16 0.30 0.28 0.24
RBMX ENST00000320676 4.82 13.73 6.66 3.61 2.05 3.01 0.30 0.60 0.32
AP1G1 ENST00000393512 4.83 4.27 2.21 3.61 3.25 4.07 0.30 0.32 0.23
PHOX2B ENST00000226382 4.83 14.36 6.95 3.60 2.02 2.90 0.30 0.61 0.33
KATNB1 ENST00000379661 4.84 33.47 17.03 3.60 0.84 1.67 0.30 1.52 0.70
GSK3B ENST00000316626 4.84 14.18 6.86 3.60 2.06 2.92 0.30 0.61 0.33
CAPZA1 ENST00000263168 4.85 15.73 7.66 3.60 1.87 2.69 0.31 0.69 0.33
RAD51 ENST00000382643 4.86 32.40 16.44 3.60 0.87 1.71 0.31 1.47 0.69
DDI2 ENST00000480945 4.86 6.49 3.10 3.59 2.63 3.92 0.31 0.37 0.24
GPR88 ENST00000315033 4.87 26.56 13.33 3.59 1.19 2.05 0.31 1.12 0.55
NMT1 ENST00000592782 4.87 11.08 5.24 3.59 2.09 3.56 0.31 0.53 0.26
ELAVL3 ENST00000359227 4.88 22.05 11.12 3.59 1.49 2.19 0.31 0.81 0.45
TFAP4 ENST00000204517 4.88 4.36 2.30 3.59 3.27 4.04 0.31 0.32 0.22
RSRC2 ENST00000331738 4.89 6.63 3.20 3.59 2.64 3.89 0.31 0.37 0.24
NCS1 ENST00000372398 4.89 29.46 14.95 3.58 1.09 1.89 0.31 1.38 0.63
KCNK3 ENST00000302909 4.90 19.21 9.50 3.58 1.48 2.30 0.31 0.76 0.40
HNRNPU ENST00000283179 4.90 1.76 1.36 3.58 3.82 4.34 0.31 0.26 0.23
KCNQ2 ENST00000359125 4.91 3.68 2.03 3.58 3.34 4.11 0.31 0.31 0.23

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.