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
AGO2 ENST00000220592 2.69 1.55 0.65 4.02 3.88 4.64 0.29 0.26 0.19
WAPAL ENST00000298767 2.86 1.56 0.72 3.95 3.88 4.58 0.30 0.26 0.20
MYCBP2 ENST00000544440 7.25 1.57 2.12 2.91 3.88 4.09 0.38 0.26 0.23
NRXN3 ENST00000554719 6.72 1.57 1.95 2.99 3.87 4.13 0.37 0.26 0.24
TRIM24 ENST00000343526 2.17 1.58 0.53 4.16 3.87 4.70 0.27 0.26 0.17
SCN8A ENST00000354534 0.20 1.58 0.12 4.50 3.87 4.87 0.16 0.26 0.18
DPYSL5 ENST00000288699 13.27 1.59 4.76 1.67 3.86 3.67 0.66 0.26 0.25
ADAM10 ENST00000260408 2.49 1.59 0.62 4.09 3.86 4.66 0.27 0.26 0.19
LPHN2 ENST00000319517 23.21 1.60 9.96 1.38 3.86 2.28 1.10 0.26 0.42
PIAS4 ENST00000262971 25.85 1.60 11.42 1.35 3.85 2.19 1.20 0.26 0.45
UBA1 ENST00000335972 14.16 1.61 5.15 1.62 3.87 3.59 0.71 0.26 0.25
DNMT1 ENST00000359526 4.46 1.61 1.19 3.71 3.87 4.44 0.29 0.26 0.21
PRKAR1A ENST00000589228 1.82 1.62 0.45 4.29 3.86 4.74 0.22 0.26 0.17
AGPS ENST00000264167 5.24 1.62 1.44 3.42 3.86 4.32 0.32 0.26 0.23
CSE1L ENST00000262982 11.84 1.63 4.04 1.64 3.86 3.75 0.60 0.26 0.23
KMT2C ENST00000262189 8.90 1.63 2.73 2.35 3.86 4.01 0.45 0.26 0.23
SLC17A7 ENST00000221485 2.09 1.64 0.52 4.22 3.85 4.70 0.25 0.26 0.17
TRERF1 ENST00000372922 15.40 1.64 5.77 1.56 3.85 3.31 0.76 0.26 0.28
HDAC5 ENST00000225983 20.17 1.65 8.26 1.53 3.85 2.57 1.00 0.26 0.37
HECTD4 ENST00000550722 13.89 1.65 5.04 1.63 3.84 3.67 0.70 0.26 0.25
PSMC2 ENST00000435765 0.46 1.66 0.18 4.38 3.84 4.89 0.17 0.26 0.18
TSC1 ENST00000298552 18.79 1.66 7.58 1.54 3.84 2.75 0.91 0.26 0.33
ZC3H7A ENST00000396516 18.72 1.67 7.56 1.53 3.83 2.75 0.91 0.26 0.33
DOT1L ENST00000398665 5.67 1.67 1.63 3.19 3.83 4.28 0.33 0.26 0.23
RAI1 ENST00000353383 43.48 1.68 20.71 0.81 3.83 1.47 1.80 0.26 0.88

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.