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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
C5orf28 ENST00000500337 54.75 93.25 77.16 0.63 0.28 0.35 1.72 0.30 0.59
PCDHGA10 ENST00000398610 54.76 42.62 47.44 0.63 0.59 0.63 1.72 1.90 1.87
RSG1 ENST00000375599 54.76 81.48 70.44 0.63 0.33 0.43 1.72 0.54 0.91
WDR81 ENST00000409644 54.77 27.02 39.27 0.63 1.23 0.80 1.72 1.12 2.04
SYPL2 ENST00000369872 54.78 66.67 61.39 0.63 0.56 0.44 1.72 1.22 1.48
CD302 ENST00000259053 54.78 79.04 68.94 0.63 0.40 0.46 1.72 0.70 1.04
ANKRD39 ENST00000393537 54.79 64.77 60.21 0.63 0.48 0.48 1.72 1.24 1.60
DCSTAMP ENST00000297581 54.79 63.21 59.19 0.63 0.47 0.49 1.72 1.31 1.68
ZFHX2 ENST00000419474 54.80 11.65 31.44 0.63 2.09 0.87 1.72 0.57 1.56
LYSMD1 ENST00000368908 54.80 57.90 56.07 0.63 0.57 0.49 1.72 1.47 1.75
IL31RA ENST00000447346 54.81 53.86 53.74 0.63 0.63 0.62 1.72 1.70 1.80
HACL1 ENST00000321169 54.81 56.46 55.21 0.63 0.52 0.51 1.72 1.54 1.75
LDLRAP1 ENST00000374338 54.82 63.17 59.20 0.63 0.47 0.49 1.72 1.31 1.68
JDP2 ENST00000267569 54.82 37.42 44.68 0.63 0.75 0.62 1.72 1.66 2.06
SLC25A35 ENST00000380067 54.83 74.31 66.24 0.63 0.53 0.52 1.72 1.01 1.20
TMUB2 ENST00000587989 54.83 80.81 70.06 0.63 0.35 0.47 1.72 0.57 0.91
FAT1 ENST00000441802 54.84 19.17 35.18 0.63 1.49 0.86 1.72 0.76 1.75
OR9A2 ENST00000350513 54.84 79.82 69.50 0.63 0.35 0.44 1.72 0.62 0.97
LAT ENST00000395461 54.85 33.30 42.35 0.65 0.84 0.70 1.72 1.51 2.02
ELMO3 ENST00000393997 54.85 53.56 53.64 0.65 0.63 0.63 1.71 1.70 1.81
HFE ENST00000357618 54.86 64.91 60.35 0.65 0.48 0.46 1.71 1.25 1.58
ZNF804B ENST00000333190 54.86 54.09 53.95 0.65 0.65 0.61 1.71 1.68 1.77
NOP9 ENST00000267425 54.87 58.23 56.31 0.63 0.54 0.49 1.71 1.43 1.75
RHBDD1 ENST00000392062 54.87 85.76 73.05 0.63 0.27 0.42 1.71 0.44 0.80
NOL9 ENST00000377705 54.88 28.22 39.89 0.63 1.19 0.78 1.72 1.22 2.02

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