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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
SPAM1 ENST00000340011 82.39 69.39 79.22 0.30 0.56 0.38 0.57 1.14 0.54
NT5DC4 ENST00000327581 82.39 51.86 69.23 0.30 0.59 0.44 0.56 1.87 0.97
OR2T1 ENST00000366474 82.40 94.26 91.26 0.30 0.24 0.15 0.56 0.25 0.18
GRIN3B ENST00000234389 82.40 54.84 71.00 0.30 0.57 0.43 0.56 1.63 0.85
CCL11 ENST00000305869 82.41 88.49 88.56 0.30 0.23 0.22 0.56 0.36 0.28
MXRA8 ENST00000309212 82.41 56.58 72.12 0.30 0.53 0.43 0.56 1.55 0.81
CDHR4 ENST00000412678 82.42 54.88 71.09 0.30 0.57 0.43 0.56 1.62 0.86
KRTAP4-12 ENST00000394014 82.42 49.58 67.90 0.30 0.66 0.51 0.56 2.03 1.11
ZNF267 ENST00000300870 82.43 81.60 85.37 0.30 0.33 0.34 0.57 0.52 0.35
LCN8 ENST00000371688 82.43 66.07 77.45 0.30 0.56 0.35 0.57 1.21 0.58
C7orf71 ENST00000409974 82.44 92.14 90.33 0.30 0.25 0.15 0.57 0.32 0.21
KRTAP5-9 ENST00000528743 82.44 95.73 91.85 0.30 0.23 0.14 0.56 0.20 0.17
SERPINA5 ENST00000329597 82.45 86.73 87.73 0.30 0.24 0.24 0.56 0.40 0.32
ZNF425 ENST00000378061 82.45 86.64 87.69 0.30 0.24 0.24 0.56 0.40 0.31
OR7A5 ENST00000322301 82.46 99.92 93.99 0.30 0.17 0.09 0.56 0.10 0.11
SNAI3 ENST00000332281 82.46 64.93 76.81 0.30 0.48 0.35 0.57 1.24 0.61
LST3 ENST00000540229 82.47 79.93 84.53 0.30 0.37 0.33 0.57 0.61 0.39
SORD ENST00000267814 82.48 71.49 80.30 0.30 0.53 0.38 0.57 1.06 0.52
MEGF6 ENST00000356575 82.48 45.55 65.58 0.30 0.73 0.51 0.57 1.99 1.30
PHRF1 ENST00000416188 82.49 16.57 48.39 0.30 1.77 0.67 0.57 0.70 1.88
C21orf33 ENST00000291577 82.49 76.85 83.02 0.30 0.42 0.32 0.56 0.81 0.40
ZNF675 ENST00000359788 82.50 62.68 75.55 0.30 0.51 0.37 0.56 1.31 0.64
OR7A10 ENST00000248058 82.50 95.29 91.71 0.30 0.23 0.14 0.56 0.21 0.18
PGLYRP2 ENST00000340880 82.51 70.73 79.94 0.30 0.48 0.35 0.56 1.08 0.52
PDCD1LG2 ENST00000397747 82.51 71.20 80.20 0.30 0.52 0.35 0.56 1.06 0.52

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