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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
SNAP25 ENST00000254976 0.97 7.64 2.04 4.37 2.49 4.12 0.18 0.42 0.23
HNRNPA3 ENST00000392524 0.90 7.64 2.01 4.36 2.49 4.12 0.18 0.42 0.23
PDS5A ENST00000303538 2.58 5.80 1.98 4.04 2.86 4.12 0.28 0.35 0.24
PPFIA2 ENST00000549396 7.27 1.26 2.00 2.91 3.99 4.12 0.38 0.27 0.23
PLCL2 ENST00000418129 7.60 0.79 1.97 2.73 4.11 4.12 0.40 0.27 0.24
NF2 ENST00000338641 7.48 0.87 1.97 2.77 4.10 4.12 0.39 0.29 0.24
RXRA ENST00000481739 5.08 3.26 1.96 3.52 3.45 4.13 0.30 0.28 0.24
PCBP2 ENST00000359462 0.45 7.90 1.96 4.39 2.53 4.13 0.17 0.44 0.24
NRXN3 ENST00000554719 6.72 1.57 1.95 2.99 3.87 4.13 0.37 0.26 0.24
KALRN ENST00000240874 5.28 3.01 1.95 3.39 3.48 4.14 0.32 0.28 0.24
ARFGEF1 ENST00000262215 5.58 2.65 1.94 3.23 3.54 4.14 0.33 0.29 0.24
GRIA3 ENST00000264357 2.92 5.30 1.94 3.91 3.11 4.14 0.30 0.32 0.24
HNRNPD ENST00000313899 0.87 7.34 1.93 4.36 2.54 4.15 0.18 0.37 0.24
KHSRP ENST00000398148 7.63 0.57 1.93 2.73 4.16 4.15 0.40 0.28 0.24
RNF2 ENST00000367510 2.23 5.97 1.92 4.17 2.82 4.15 0.28 0.35 0.24
USP48 ENST00000308271 4.57 3.61 1.92 3.68 3.37 4.15 0.29 0.30 0.24
PELP1 ENST00000574876 4.82 3.36 1.91 3.61 3.44 4.16 0.30 0.28 0.24
ELAVL1 ENST00000407627 0.96 7.23 1.91 4.37 2.59 4.16 0.18 0.37 0.24
MED1 ENST00000300651 6.46 1.71 1.90 3.05 3.85 4.16 0.37 0.26 0.24
GRIN2A ENST00000396573 3.02 5.14 1.90 3.88 3.21 4.17 0.30 0.33 0.24
TAOK1 ENST00000261716 1.34 6.80 1.89 4.35 2.66 4.17 0.18 0.37 0.24
PPFIA3 ENST00000334186 6.11 2.00 1.89 3.02 3.72 4.17 0.34 0.28 0.24
ACTB ENST00000331789 0.04 8.06 1.88 4.60 2.53 4.18 0.15 0.44 0.24
SMARCB1 ENST00000263121 1.03 7.06 1.87 4.36 2.57 4.18 0.18 0.37 0.24
CHD7 ENST00000423902 7.71 0.35 1.87 2.73 4.14 4.18 0.40 0.28 0.24

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