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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
BTBD19 ENST00000450269 59.20 32.13 44.08 0.53 0.87 0.61 1.46 1.46 2.04
COBLL1 ENST00000342193 59.26 20.64 38.25 0.56 1.46 0.85 1.46 0.78 2.04
ARFGAP1 ENST00000353546 61.44 30.58 44.55 0.67 1.08 0.62 1.31 1.39 2.04
NAPG ENST00000322897 62.22 29.68 44.49 0.68 1.13 0.61 1.27 1.39 2.04
SLC5A5 ENST00000222248 62.82 29.05 44.44 0.59 1.14 0.61 1.29 1.31 2.04
ATP10A ENST00000356865 62.96 22.25 40.78 0.58 1.53 0.81 1.27 0.82 2.04
ATOH8 ENST00000306279 63.36 17.69 38.82 0.59 1.54 0.82 1.24 0.73 2.04
HDGFRP2 ENST00000301284 64.08 18.37 39.58 0.57 1.48 0.80 1.20 0.75 2.04
CHPF ENST00000243776 65.08 27.71 45.03 0.54 1.27 0.70 1.15 1.18 2.04
INCENP ENST00000394818 65.35 14.86 38.39 0.56 1.92 0.84 1.12 0.62 2.04
NAP1L2 ENST00000373517 65.37 26.32 44.31 0.56 1.19 0.61 1.12 1.08 2.04
MSANTD1 ENST00000438480 66.65 24.67 44.08 0.62 1.29 0.61 1.05 1.04 2.04
KNDC1 ENST00000304613 66.77 15.87 39.70 0.59 1.89 0.78 1.05 0.68 2.04
NHSL1 ENST00000427025 67.52 17.70 40.77 0.57 1.54 0.81 1.06 0.73 2.04
SIRPA ENST00000358771 68.08 16.55 40.53 0.57 1.78 0.80 1.02 0.69 2.04
PIEZO2 ENST00000503781 69.09 16.51 41.02 0.57 1.78 0.76 0.96 0.69 2.04
LIN7B ENST00000221459 70.49 21.34 44.40 0.49 1.43 0.59 0.91 0.80 2.04
SCAF1 ENST00000360565 73.00 9.52 39.62 0.33 2.51 0.78 0.79 0.49 2.04
ADARB2 ENST00000381312 75.15 17.44 44.95 0.38 1.59 0.68 0.76 0.74 2.04
AATK ENST00000326724 75.30 17.27 44.95 0.37 1.61 0.68 0.75 0.75 2.04
ZNF541 ENST00000314121 76.38 3.54 38.25 0.33 3.38 0.85 0.74 0.30 2.04
GSE1 ENST00000253458 78.27 2.17 38.51 0.35 3.65 0.84 0.67 0.29 2.04
EFHC2 ENST00000420999 82.05 3.20 40.79 0.30 3.46 0.81 0.57 0.28 2.04
WDR18 ENST00000251289 82.52 9.19 44.33 0.30 2.48 0.61 0.56 0.46 2.04
BLCAP ENST00000414542 7.61 72.18 38.19 2.73 0.52 0.85 0.40 1.04 2.04

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