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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
RMI1 ENST00000325875 36.38 48.93 40.84 0.96 0.65 0.80 1.81 2.04 2.05
CEP41 ENST00000223208 37.14 48.97 41.30 0.94 0.65 0.73 1.73 2.04 2.02
TTC14 ENST00000296015 41.67 46.36 42.26 0.81 0.73 0.70 1.71 2.04 2.01
ADCY4 ENST00000310677 46.52 46.38 45.10 0.56 0.73 0.70 1.81 2.04 2.02
UTP23 ENST00000309822 46.83 49.16 46.66 0.56 0.66 0.66 1.81 2.04 1.87
CPLX3 ENST00000395018 47.23 46.13 45.39 0.56 0.73 0.70 1.82 2.04 2.01
CCHCR1 ENST00000396268 49.38 46.15 46.41 0.57 0.73 0.67 1.80 2.04 1.91
SELT ENST00000471696 49.79 46.28 46.75 0.54 0.73 0.67 1.83 2.04 1.87
AQP1 ENST00000311813 51.70 49.15 49.32 0.58 0.66 0.70 1.82 2.04 1.85
ACSS3 ENST00000548058 54.35 48.95 50.72 0.65 0.65 0.66 1.73 2.04 1.84
SYNC ENST00000409190 57.72 46.16 51.01 0.57 0.73 0.66 1.55 2.04 1.87
NDUFAF1 ENST00000260361 58.03 48.90 52.79 0.56 0.63 0.61 1.53 2.04 1.88
TTC3 ENST00000399017 58.39 46.27 51.47 0.56 0.73 0.63 1.52 2.04 1.92
ROBO4 ENST00000306534 59.80 49.16 53.94 0.59 0.66 0.61 1.39 2.04 1.77
MRPS27 ENST00000261413 60.99 46.15 52.94 0.58 0.73 0.61 1.34 2.04 1.87
PALD1 ENST00000263563 63.81 46.27 54.61 0.59 0.73 0.56 1.22 2.04 1.74
MFAP5 ENST00000359478 64.66 46.29 55.05 0.54 0.73 0.51 1.19 2.04 1.74
RNF133 ENST00000340112 65.97 46.28 55.81 0.59 0.73 0.52 1.06 2.04 1.74
KIAA0556 ENST00000261588 66.94 48.89 57.98 0.61 0.63 0.47 1.04 2.04 1.68
MGME1 ENST00000377710 67.36 46.33 56.65 0.58 0.73 0.52 1.04 2.04 1.71
CHDH ENST00000315251 68.13 49.18 58.76 0.57 0.66 0.52 1.02 2.04 1.65
OR52I2 ENST00000312614 69.85 49.17 59.91 0.53 0.66 0.49 0.95 2.04 1.63
ZNF699 ENST00000591998 75.97 46.37 61.92 0.34 0.73 0.48 0.76 2.04 1.45
FBF1 ENST00000319129 76.45 46.31 62.18 0.33 0.73 0.48 0.73 2.04 1.45
DOK7 ENST00000340083 77.05 46.14 62.45 0.34 0.73 0.48 0.73 2.04 1.39

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