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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
LYNX1 ENST00000335822 44.55 73.20 58.99 0.65 0.54 0.48 1.80 1.02 1.65
BAG5 ENST00000337322 44.56 69.64 56.97 0.65 0.53 0.49 1.80 1.12 1.72
MICU3 ENST00000318063 44.56 54.29 48.30 0.65 0.62 0.67 1.80 1.69 1.88
C11orf54 ENST00000528288 44.57 79.30 62.98 0.65 0.38 0.51 1.80 0.67 1.40
RND2 ENST00000587250 44.57 65.56 54.65 0.65 0.53 0.56 1.80 1.22 1.73
KDM4C ENST00000381309 44.58 26.65 33.77 0.65 1.19 0.89 1.80 1.12 1.74
TIMM17A ENST00000367287 44.58 35.44 38.32 0.65 0.77 0.85 1.80 1.56 2.04
WNT10B ENST00000301061 44.59 51.78 46.91 0.65 0.61 0.70 1.80 1.89 1.87
PTCH2 ENST00000372192 44.59 46.34 43.83 0.65 0.73 0.61 1.80 2.05 2.01
MYO3B ENST00000408978 44.60 54.61 48.48 0.65 0.58 0.68 1.80 1.66 1.86
APTX ENST00000379813 44.61 73.77 59.46 0.65 0.53 0.49 1.80 1.02 1.70
SNTN ENST00000343837 44.61 87.53 68.00 0.65 0.23 0.51 1.79 0.37 1.10
COMMD9 ENST00000263401 44.62 35.88 38.53 0.65 0.80 0.84 1.79 1.58 2.03
MYOF ENST00000359263 44.62 49.81 45.90 0.65 0.66 0.70 1.79 2.02 1.98
PGM1 ENST00000371083 44.63 69.97 57.20 0.65 0.53 0.52 1.78 1.14 1.69
BCL6B ENST00000293805 44.63 29.85 35.45 0.65 1.13 0.87 1.78 1.40 1.77
RPP14 ENST00000445193 44.64 73.27 59.13 0.65 0.56 0.51 1.78 1.02 1.68
TIMM22 ENST00000327158 44.64 84.20 66.07 0.65 0.27 0.51 1.78 0.44 1.23
CROT ENST00000419147 44.65 62.72 53.11 0.65 0.51 0.61 1.78 1.31 1.87
PLEKHA1 ENST00000368990 44.65 38.63 39.99 0.65 0.72 0.81 1.78 1.66 1.99
ADH5 ENST00000296412 44.66 77.29 61.69 0.65 0.42 0.46 1.78 0.77 1.46
TRIT1 ENST00000316891 44.66 66.55 55.20 0.65 0.56 0.51 1.78 1.22 1.75
B4GALT1 ENST00000379731 44.67 36.32 38.76 0.65 0.82 0.82 1.78 1.62 2.03
FOXN2 ENST00000340553 44.67 24.33 32.67 0.65 1.33 0.86 1.78 1.00 1.63
METTL1 ENST00000324871 44.68 57.75 50.25 0.65 0.57 0.65 1.77 1.47 1.92

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