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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
HEMK1 ENST00000232854 55.40 58.10 56.56 0.61 0.53 0.52 1.66 1.46 1.70
OR4D6 ENST00000300127 55.41 79.60 69.71 0.61 0.38 0.44 1.66 0.66 0.94
CRIPT ENST00000238892 55.41 82.44 71.43 0.61 0.34 0.46 1.67 0.52 0.87
COMMD3 ENST00000376836 55.42 62.52 59.15 0.61 0.53 0.49 1.66 1.31 1.68
MMP19 ENST00000322569 55.42 78.27 68.88 0.61 0.43 0.46 1.66 0.74 1.04
TOMM7 ENST00000358435 55.43 88.90 75.09 0.61 0.25 0.39 1.66 0.35 0.67
SLC6A13 ENST00000343164 55.43 55.21 54.90 0.61 0.57 0.51 1.65 1.62 1.74
CPA6 ENST00000297770 55.44 67.60 62.36 0.61 0.53 0.48 1.65 1.19 1.41
SMCO3 ENST00000316048 55.44 83.23 71.95 0.61 0.28 0.43 1.66 0.47 0.81
PFKFB1 ENST00000375006 55.45 54.18 54.36 0.61 0.62 0.59 1.66 1.69 1.75
ARMC2 ENST00000392644 55.45 42.76 47.95 0.61 0.62 0.67 1.66 1.92 1.88
ACAD9 ENST00000308982 55.46 46.21 49.78 0.61 0.73 0.65 1.65 2.04 1.87
APPL2 ENST00000551662 55.46 60.51 58.05 0.61 0.52 0.47 1.65 1.41 1.66
PRR15L ENST00000300557 55.47 75.39 67.20 0.61 0.46 0.52 1.66 0.89 1.16
STK33 ENST00000447869 55.47 43.21 48.21 0.61 0.62 0.66 1.65 1.92 1.87
TVP23C-CDRT4 ENST00000522212 55.48 74.67 66.79 0.61 0.54 0.53 1.65 0.97 1.20
MON1B ENST00000248248 55.48 31.53 41.72 0.61 0.96 0.72 1.65 1.42 2.01
EOGT ENST00000295571 55.49 54.45 54.52 0.61 0.61 0.57 1.65 1.66 1.75
F13B ENST00000367412 55.49 44.41 48.86 0.61 0.61 0.71 1.66 1.97 1.85
LRRC46 ENST00000269025 55.50 50.43 52.19 0.61 0.65 0.61 1.66 1.95 1.89
MARC2 ENST00000366913 55.50 56.23 55.53 0.61 0.52 0.52 1.66 1.56 1.74
LYG1 ENST00000409448 55.51 73.83 66.37 0.61 0.53 0.53 1.66 1.02 1.20
TRPV3 ENST00000301365 55.51 64.54 60.57 0.61 0.47 0.44 1.66 1.22 1.58
KRT36 ENST00000328119 55.52 75.34 67.20 0.61 0.48 0.52 1.66 0.90 1.16
CYP2U1 ENST00000332884 55.52 37.96 45.46 0.61 0.78 0.70 1.66 1.70 1.98

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