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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
AHI1 ENST00000367800 66.76 50.96 58.97 0.59 0.65 0.49 1.05 1.93 1.65
CCDC39 ENST00000442201 66.77 40.55 53.09 0.59 0.63 0.61 1.05 1.77 1.87
KNDC1 ENST00000304613 66.77 15.87 39.70 0.59 1.89 0.78 1.05 0.68 2.04
DGCR14 ENST00000252137 66.78 51.93 59.70 0.59 0.61 0.49 1.05 1.85 1.66
SLC19A3 ENST00000258403 66.78 30.81 47.59 0.59 1.06 0.65 1.05 1.37 1.88
SLC2A14 ENST00000543909 66.79 33.56 49.10 0.59 0.85 0.72 1.05 1.53 1.83
HEPH ENST00000519389 66.79 27.29 45.74 0.59 1.25 0.67 1.05 1.15 1.98
ANG ENST00000336811 66.80 93.63 83.55 0.59 0.28 0.33 1.05 0.28 0.40
PSMB11 ENST00000408907 66.80 89.90 81.73 0.59 0.25 0.35 1.05 0.36 0.47
CHRNA7 ENST00000454250 66.81 39.39 52.34 0.59 0.70 0.61 1.05 1.65 1.90
CCL4 ENST00000250151 66.81 80.11 76.55 0.59 0.37 0.38 1.05 0.60 0.61
FOLR1 ENST00000393679 66.82 36.31 50.60 0.59 0.82 0.66 1.05 1.61 1.86
HIST1H2BJ ENST00000607124 66.83 92.40 82.96 0.59 0.25 0.32 1.05 0.30 0.40
CWF19L2 ENST00000282251 66.83 41.42 53.55 0.59 0.62 0.63 1.05 1.80 1.80
KCNH6 ENST00000583023 66.84 76.19 74.42 0.59 0.43 0.40 1.05 0.85 0.70
REM1 ENST00000201979 66.84 76.11 74.33 0.59 0.43 0.40 1.05 0.86 0.70
SLAMF1 ENST00000302035 66.85 42.25 54.05 0.59 0.61 0.59 1.05 1.89 1.77
HIST1H2BM ENST00000359465 66.85 97.28 85.42 0.59 0.23 0.34 1.04 0.19 0.35
HHATL ENST00000441594 66.86 47.44 57.02 0.59 0.65 0.51 1.04 2.02 1.70
PTPRC ENST00000442510 66.86 5.10 34.19 0.59 3.20 0.87 1.04 0.33 1.75
BLOC1S5 ENST00000397457 66.87 92.21 82.90 0.59 0.25 0.32 1.04 0.31 0.40
PMVK ENST00000368467 66.87 76.20 74.45 0.59 0.43 0.40 1.04 0.85 0.69
ANKRD35 ENST00000355594 66.88 61.93 66.06 0.59 0.56 0.51 1.04 1.36 1.23
PGLS ENST00000252603 66.88 68.15 69.73 0.61 0.53 0.44 1.04 1.22 0.93
OR1N2 ENST00000373688 66.89 89.08 81.33 0.61 0.27 0.38 1.04 0.35 0.49

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