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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
TMEM43 ENST00000306077 57.34 69.94 65.08 0.56 0.53 0.51 1.57 1.15 1.31
S100A1 ENST00000292169 57.34 91.91 77.82 0.57 0.23 0.38 1.56 0.32 0.54
SGCD ENST00000337851 57.35 42.92 49.02 0.57 0.63 0.72 1.56 1.91 1.83
MCUR1 ENST00000379170 57.35 64.31 61.57 0.57 0.49 0.46 1.56 1.20 1.48
C11orf52 ENST00000278601 57.36 85.63 74.37 0.57 0.27 0.40 1.56 0.44 0.70
BLVRB ENST00000263368 57.36 85.07 74.03 0.57 0.25 0.38 1.56 0.45 0.69
MRPL27 ENST00000225969 57.37 41.95 48.53 0.57 0.61 0.68 1.55 1.83 1.86
GPC2 ENST00000292377 57.37 29.88 41.84 0.57 1.13 0.68 1.55 1.40 2.02
OR2AT4 ENST00000305159 57.38 82.33 72.53 0.57 0.34 0.46 1.55 0.52 0.83
METTL20 ENST00000357721 57.38 87.99 75.67 0.57 0.25 0.38 1.55 0.37 0.64
TIFA ENST00000361717 57.39 63.65 61.12 0.57 0.49 0.43 1.55 1.23 1.51
YIF1A ENST00000376901 57.39 82.51 72.63 0.57 0.34 0.46 1.55 0.52 0.81
PKDCC ENST00000294964 57.40 50.13 53.18 0.57 0.67 0.61 1.55 1.99 1.88
SCTR ENST00000019103 57.40 60.63 59.21 0.57 0.53 0.49 1.55 1.41 1.68
EMILIN3 ENST00000332312 57.41 46.44 50.98 0.57 0.73 0.66 1.55 2.02 1.85
ATP10B ENST00000327245 57.41 55.68 56.32 0.57 0.52 0.49 1.55 1.60 1.75
CSRP2 ENST00000311083 57.42 81.76 72.27 0.58 0.34 0.44 1.55 0.51 0.82
PDCD2L ENST00000246535 57.42 60.91 59.43 0.58 0.56 0.49 1.55 1.40 1.70
SLC10A5 ENST00000518568 57.43 87.26 75.25 0.58 0.22 0.37 1.55 0.41 0.67
FSTL3 ENST00000166139 57.44 17.66 35.69 0.58 1.58 0.85 1.55 0.73 1.76
NUPL2 ENST00000258742 57.44 68.62 64.30 0.58 0.53 0.51 1.55 1.18 1.35
HOGA1 ENST00000370646 57.45 88.87 76.18 0.58 0.25 0.37 1.55 0.35 0.62
NIPAL3 ENST00000374399 57.45 47.01 51.35 0.58 0.68 0.63 1.54 1.98 1.92
QPCTL ENST00000012049 57.46 75.56 68.50 0.58 0.44 0.47 1.54 0.90 1.06
PER2 ENST00000254657 57.46 14.28 34.06 0.58 2.06 0.91 1.54 0.61 1.73

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