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
ZFAND2A ENST00000316495 79.80 84.91 85.67 0.33 0.27 0.33 0.58 0.44 0.34
MFSD9 ENST00000258436 79.81 77.47 82.02 0.33 0.42 0.37 0.58 0.77 0.46
TCF3 ENST00000262965 79.82 22.72 50.29 0.32 1.47 0.65 0.58 0.88 1.92
VMO1 ENST00000328739 79.82 92.93 89.49 0.32 0.29 0.18 0.58 0.30 0.23
KRTAP4-7 ENST00000391417 79.83 94.43 90.19 0.32 0.23 0.18 0.58 0.24 0.21
KCNV2 ENST00000382082 79.83 97.29 91.45 0.32 0.23 0.15 0.58 0.19 0.18
CAPN14 ENST00000403897 79.84 57.20 70.86 0.32 0.56 0.43 0.58 1.48 0.86
LAMTOR5 ENST00000256644 79.84 87.59 86.90 0.32 0.23 0.29 0.58 0.37 0.31
CHTF8 ENST00000574807 79.85 25.57 51.89 0.32 1.25 0.62 0.58 1.05 1.94
METTL12 ENST00000532971 79.85 73.64 80.08 0.32 0.52 0.35 0.58 1.03 0.52
MSR1 ENST00000262101 79.86 84.23 85.40 0.30 0.28 0.34 0.58 0.44 0.35
U82695.9 ENST00000428676 79.86 95.58 90.80 0.30 0.23 0.15 0.58 0.21 0.20
MRPL54 ENST00000330133 79.87 78.47 82.57 0.30 0.43 0.32 0.58 0.74 0.43
C1orf131 ENST00000366649 79.87 86.55 86.40 0.30 0.24 0.32 0.58 0.42 0.33
RSPH6A ENST00000221538 79.88 54.04 69.03 0.30 0.65 0.46 0.58 1.69 1.03
FOXE3 ENST00000335071 79.88 65.63 75.76 0.30 0.53 0.38 0.58 1.22 0.64
ISM2 ENST00000342219 79.89 68.36 77.29 0.30 0.52 0.35 0.58 1.21 0.58
C15orf40 ENST00000451195 79.89 61.51 73.50 0.30 0.54 0.40 0.58 1.40 0.75
C11orf74 ENST00000532470 79.90 85.58 85.98 0.30 0.27 0.33 0.58 0.44 0.33
OR6C70 ENST00000327335 79.90 96.55 91.19 0.30 0.22 0.15 0.59 0.19 0.18
PDHA2 ENST00000295266 79.91 88.18 87.22 0.30 0.23 0.28 0.59 0.37 0.31
ZNF302 ENST00000505242 79.91 56.43 70.49 0.30 0.52 0.43 0.59 1.53 0.91
LTF ENST00000231751 79.92 65.93 75.94 0.30 0.54 0.38 0.58 1.24 0.62
ARGFX ENST00000334384 79.92 91.49 88.83 0.30 0.23 0.19 0.58 0.32 0.28
B3GNTL1 ENST00000320865 79.93 88.96 87.58 0.30 0.25 0.27 0.58 0.35 0.31

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.