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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
LRRN4 ENST00000378858 84.58 73.15 82.23 0.29 0.53 0.35 0.46 1.01 0.44
GUCA2A ENST00000357001 84.59 71.34 81.32 0.29 0.53 0.38 0.46 1.05 0.48
KIAA1614 ENST00000367588 84.59 57.82 74.00 0.29 0.57 0.39 0.46 1.48 0.70
C16orf59 ENST00000361837 84.60 72.94 82.15 0.29 0.51 0.35 0.46 1.02 0.45
CTB-186H2.3 ENST00000591669 84.60 99.24 94.51 0.29 0.15 0.10 0.46 0.13 0.12
NAPRT1 ENST00000449291 84.61 75.24 83.27 0.29 0.49 0.29 0.46 0.90 0.40
WDR60 ENST00000407559 84.61 32.58 58.72 0.29 0.86 0.52 0.46 1.48 1.65
MT1M ENST00000379818 84.62 95.24 92.67 0.29 0.23 0.14 0.46 0.21 0.15
CTAGE6 ENST00000470691 84.62 99.38 94.77 0.29 0.16 0.09 0.46 0.12 0.11
FAM53A ENST00000308132 84.63 66.32 78.72 0.29 0.54 0.38 0.47 1.20 0.54
AZGP1 ENST00000292401 84.63 79.99 85.64 0.29 0.37 0.32 0.47 0.61 0.35
ZNF71 ENST00000328070 84.64 67.50 79.37 0.29 0.54 0.39 0.47 1.20 0.53
NXF5 ENST00000537026 84.64 84.99 87.94 0.29 0.25 0.24 0.47 0.45 0.32
KRTAP24-1 ENST00000340345 84.65 95.04 92.59 0.29 0.23 0.14 0.47 0.21 0.15
VIMP ENST00000398226 84.65 88.27 89.59 0.29 0.23 0.18 0.47 0.37 0.23
TCL1A ENST00000402399 84.66 94.40 92.21 0.29 0.23 0.14 0.47 0.24 0.16
CFH ENST00000367429 84.67 13.03 47.65 0.29 2.07 0.65 0.47 0.59 1.88
PLAC1 ENST00000359237 84.67 97.60 93.93 0.29 0.22 0.09 0.47 0.20 0.11
C21orf2 ENST00000397956 84.68 75.59 83.50 0.29 0.44 0.33 0.47 0.90 0.40
KRTAP10-8 ENST00000334662 84.68 83.87 87.44 0.29 0.28 0.28 0.47 0.47 0.31
RBBP8NL ENST00000252998 84.69 21.89 52.59 0.29 1.46 0.61 0.47 0.81 1.89
KRTAP19-7 ENST00000334849 84.69 98.35 94.17 0.29 0.21 0.09 0.47 0.14 0.12
EML6 ENST00000356458 84.70 20.37 51.67 0.29 1.44 0.62 0.47 0.76 1.94
OR1C1 ENST00000408896 84.70 83.35 87.20 0.29 0.27 0.28 0.47 0.48 0.31
ZNF780A ENST00000455521 84.71 92.05 91.28 0.29 0.24 0.15 0.47 0.33 0.18

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