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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
CHST4 ENST00000338482 68.31 87.58 81.31 0.56 0.23 0.38 1.00 0.37 0.48
NMRAL1 ENST00000574733 68.32 71.71 72.72 0.56 0.51 0.43 1.00 1.07 0.81
OR6A2 ENST00000332601 68.32 62.46 67.18 0.56 0.54 0.52 1.00 1.31 1.17
WDR93 ENST00000268130 68.33 62.63 67.26 0.56 0.51 0.52 1.00 1.31 1.16
ASB16 ENST00000293414 68.33 83.34 79.16 0.56 0.27 0.38 1.00 0.48 0.54
SLC16A5 ENST00000450736 68.34 81.42 78.10 0.56 0.33 0.39 1.00 0.55 0.55
ZNF514 ENST00000295208 68.34 76.55 75.37 0.56 0.42 0.37 0.99 0.83 0.66
OTUD1 ENST00000376495 68.35 33.18 49.69 0.56 0.82 0.66 0.99 1.51 1.84
VGLL1 ENST00000370634 68.35 28.65 47.25 0.56 1.19 0.66 0.99 1.29 1.87
GPX1 ENST00000419783 68.36 93.06 84.00 0.56 0.28 0.35 0.99 0.30 0.42
SELK ENST00000495461 68.36 87.50 81.30 0.56 0.23 0.38 0.99 0.38 0.48
IL17F ENST00000336123 68.37 66.02 69.33 0.56 0.56 0.43 0.99 1.21 0.98
CALCR ENST00000359558 68.37 44.52 56.21 0.56 0.65 0.49 0.99 1.98 1.77
PRCP ENST00000393399 68.38 65.03 68.72 0.56 0.51 0.46 0.99 1.24 1.05
CD164L2 ENST00000374027 68.38 84.33 79.61 0.57 0.28 0.38 0.99 0.44 0.53
CNGB3 ENST00000320005 68.39 53.18 61.47 0.57 0.66 0.44 0.99 1.75 1.47
CAPS2 ENST00000409445 68.40 70.80 72.29 0.57 0.49 0.43 0.99 1.08 0.82
PRSS53 ENST00000280606 68.40 74.30 74.22 0.57 0.53 0.39 0.98 1.01 0.69
SPPL2C ENST00000329196 68.41 58.32 64.75 0.57 0.54 0.49 0.98 1.41 1.32
LAMB4 ENST00000388781 68.41 55.84 63.25 0.57 0.52 0.49 0.98 1.58 1.36
SLC25A48 ENST00000412661 68.42 85.16 80.12 0.57 0.25 0.35 0.98 0.45 0.53
HIST1H2BE ENST00000356530 68.42 97.37 86.12 0.57 0.22 0.33 0.98 0.19 0.33
DDN ENST00000421952 68.43 24.14 44.93 0.57 1.35 0.68 0.98 0.99 2.03
NOTUM ENST00000409678 68.43 30.18 48.18 0.57 1.10 0.66 0.98 1.41 1.87
SNTG2 ENST00000308624 68.44 66.01 69.37 0.57 0.56 0.43 0.98 1.22 0.98

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