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
SDHA ENST00000264932 43.00 47.14 43.49 0.82 0.66 0.62 1.77 2.00 2.00
KLF16 ENST00000250916 43.01 81.57 63.46 0.82 0.33 0.51 1.78 0.52 1.38
TTLL4 ENST00000392102 43.01 36.94 38.29 0.82 0.75 0.85 1.78 1.70 2.04
ATP12A ENST00000218548 43.02 43.71 41.59 0.82 0.62 0.73 1.78 1.96 1.99
C1orf74 ENST00000294811 43.02 60.49 50.82 0.82 0.52 0.67 1.77 1.41 1.84
TPRG1L ENST00000378344 43.03 79.09 61.80 0.82 0.39 0.47 1.77 0.69 1.46
GTF2H5 ENST00000607778 43.03 86.96 66.73 0.82 0.22 0.54 1.77 0.40 1.20
ANO10 ENST00000292246 43.04 62.67 52.10 0.82 0.51 0.61 1.77 1.31 1.92
MED30 ENST00000297347 43.05 39.51 39.61 0.82 0.68 0.78 1.77 1.63 2.04
CBX2 ENST00000310942 43.05 5.94 22.64 0.82 2.83 1.18 1.77 0.35 0.96
AGTR1 ENST00000542281 43.06 73.03 58.10 0.82 0.51 0.47 1.77 1.03 1.65
RASGRP3 ENST00000403687 43.06 24.65 32.04 0.82 1.29 0.90 1.77 1.05 1.60
GATSL2 ENST00000426327 43.07 85.80 66.10 0.82 0.28 0.51 1.77 0.44 1.21
CA13 ENST00000321764 43.07 62.32 51.86 0.82 0.53 0.62 1.77 1.33 1.92
TBCB ENST00000221855 43.08 48.86 44.51 0.82 0.65 0.61 1.77 2.03 2.04
NPC1L1 ENST00000289547 43.08 49.79 45.12 0.82 0.66 0.70 1.77 2.03 2.01
YAE1D1 ENST00000223273 43.09 59.24 50.16 0.82 0.49 0.63 1.77 1.44 1.90
MRTO4 ENST00000330263 43.09 7.76 23.53 0.82 2.53 1.18 1.78 0.43 1.01
ABCC1 ENST00000399410 43.10 17.53 28.49 0.82 1.58 0.78 1.78 0.73 1.29
SLC22A7 ENST00000372585 43.10 58.38 49.67 0.82 0.54 0.66 1.79 1.41 1.84
OAZ3 ENST00000321531 43.11 76.91 60.54 0.82 0.43 0.44 1.79 0.79 1.58
ARG2 ENST00000261783 43.11 48.56 44.30 0.82 0.65 0.61 1.79 2.01 2.04
PSPH ENST00000395471 43.12 63.92 52.81 0.82 0.48 0.61 1.79 1.21 1.88
FAM136A ENST00000037869 43.12 87.85 67.27 0.82 0.24 0.52 1.79 0.38 1.15
IRX2 ENST00000382611 43.13 35.71 37.66 0.82 0.78 0.82 1.79 1.58 2.00

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.