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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
TCF19 ENST00000376257 33.71 66.05 48.78 0.94 0.56 0.70 1.70 1.21 1.86
PM20D2 ENST00000275072 33.71 55.02 42.64 0.94 0.57 0.68 1.70 1.63 2.02
AAR2 ENST00000373932 33.72 73.37 52.87 0.94 0.54 0.61 1.70 1.03 1.87
SNX30 ENST00000374232 33.72 23.15 26.54 0.94 1.46 0.99 1.70 0.90 1.26
MED19 ENST00000337672 33.73 31.39 30.81 0.94 0.96 0.78 1.69 1.41 1.49
TPD52L1 ENST00000534000 33.73 69.05 50.42 0.95 0.54 0.67 1.69 1.14 1.89
DSP ENST00000379802 33.74 9.75 19.79 0.95 2.43 1.49 1.70 0.50 0.85
ZNF12 ENST00000405858 33.74 25.63 27.85 0.95 1.24 0.87 1.70 1.05 1.28
ANGEL1 ENST00000251089 33.75 41.43 35.73 0.95 0.62 0.85 1.70 1.81 1.77
BNIPL ENST00000368931 33.75 66.00 48.76 0.95 0.54 0.68 1.70 1.22 1.85
APBA1 ENST00000265381 33.76 15.55 22.78 0.95 1.87 1.19 1.70 0.67 0.98
ZNF420 ENST00000337995 33.76 55.60 43.05 0.95 0.53 0.66 1.70 1.60 2.01
PKP4 ENST00000389759 33.77 34.85 32.50 0.95 0.76 0.89 1.70 1.55 1.62
NME1 ENST00000336097 33.77 67.44 49.52 0.94 0.54 0.67 1.71 1.20 1.84
POLE ENST00000320574 33.78 32.39 31.33 0.92 0.87 0.87 1.72 1.47 1.55
NDC1 ENST00000371429 33.78 8.17 18.98 0.92 2.57 1.54 1.72 0.44 0.83
LEMD2 ENST00000293760 33.79 20.05 24.96 0.92 1.43 1.02 1.72 0.73 1.14
NPHS2 ENST00000367615 33.79 64.76 48.15 0.92 0.48 0.66 1.72 1.24 1.87
MFAP3 ENST00000436816 33.80 62.31 46.77 0.92 0.53 0.67 1.72 1.33 1.87
FAM53B ENST00000337318 33.81 19.42 24.66 0.92 1.46 1.05 1.73 0.74 1.10
TBX19 ENST00000367821 33.81 51.94 41.09 0.92 0.61 0.76 1.73 1.85 2.06
CCSER2 ENST00000224756 33.82 17.85 23.88 0.92 1.51 1.09 1.73 0.72 1.04
ZNF576 ENST00000336564 33.82 90.59 63.32 0.92 0.25 0.48 1.73 0.37 1.36
FNTA ENST00000302279 33.83 7.30 18.51 0.92 2.57 1.62 1.73 0.37 0.81
DOLK ENST00000372586 33.83 50.38 40.37 0.91 0.66 0.80 1.73 1.95 2.02

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