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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
PLEKHG5 ENST00000537245 33.84 29.51 29.85 0.91 1.10 0.86 1.73 1.39 1.44
TMEM251 ENST00000415050 33.84 73.28 52.92 0.91 0.56 0.61 1.73 1.02 1.87
KCNS3 ENST00000403915 33.85 49.55 40.04 0.91 0.66 0.82 1.73 2.03 1.98
MELK ENST00000298048 33.85 69.31 50.62 0.91 0.56 0.66 1.73 1.14 1.85
ZNF622 ENST00000308683 33.86 28.80 29.51 0.92 1.14 0.84 1.73 1.30 1.38
TSC22D3 ENST00000372383 33.86 49.39 39.96 0.92 0.65 0.81 1.73 2.01 2.00
HTR7 ENST00000336152 33.87 35.37 32.79 0.92 0.77 0.85 1.73 1.56 1.64
GLP2R ENST00000262441 33.87 47.91 39.26 0.92 0.59 0.80 1.73 1.99 2.04
FAM58A ENST00000406277 33.88 17.91 23.95 0.92 1.54 1.09 1.73 0.73 1.05
ACSF2 ENST00000300441 33.88 35.25 32.75 0.92 0.76 0.86 1.73 1.57 1.65
FOXJ1 ENST00000322957 33.89 10.77 20.40 0.92 2.13 1.49 1.73 0.51 0.88
PARVA ENST00000334956 33.89 23.67 26.96 0.92 1.40 1.00 1.73 0.93 1.27
NUMB ENST00000355058 33.90 31.00 30.69 0.92 1.04 0.80 1.73 1.36 1.49
SFRP1 ENST00000220772 33.90 11.15 20.64 0.92 2.09 1.48 1.73 0.54 0.88
SNIP1 ENST00000296215 33.91 27.44 28.81 0.92 1.25 0.80 1.73 1.17 1.32
APOM ENST00000375916 33.91 65.67 48.70 0.92 0.53 0.68 1.73 1.22 1.85
CLDN19 ENST00000296387 33.92 50.38 40.42 0.92 0.66 0.80 1.74 1.95 2.02
KIAA0930 ENST00000251993 33.92 45.90 38.21 0.92 0.75 0.85 1.75 2.02 2.04
HOXA13 ENST00000222753 33.93 12.44 21.28 0.92 2.06 1.39 1.75 0.59 0.91
WNT5B ENST00000397196 33.93 24.99 27.60 0.92 1.33 0.97 1.75 1.05 1.26
GPBP1L1 ENST00000355105 33.94 24.09 27.17 0.92 1.37 0.99 1.75 0.98 1.25
STXBP4 ENST00000376352 33.94 59.05 45.15 0.92 0.51 0.70 1.75 1.43 2.00
GABRD ENST00000378585 33.95 8.62 19.28 0.92 2.49 1.52 1.76 0.47 0.85
MYH4 ENST00000255381 33.95 56.71 43.69 0.92 0.53 0.61 1.76 1.56 2.01
ZNF566 ENST00000454319 33.96 25.49 27.88 0.92 1.25 0.85 1.76 1.06 1.29

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