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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
PIH1D2 ENST00000280350 43.52 77.73 61.30 0.81 0.42 0.44 1.80 0.79 1.48
POFUT2 ENST00000349485 43.53 32.71 36.24 0.80 0.84 0.86 1.80 1.45 1.84
KRT25 ENST00000312150 43.53 60.80 51.26 0.80 0.56 0.63 1.80 1.39 1.92
APLP2 ENST00000263574 43.54 18.22 29.04 0.80 1.49 0.82 1.80 0.74 1.32
TIGD5 ENST00000504548 43.54 49.04 44.93 0.80 0.66 0.68 1.80 2.03 2.03
HCN3 ENST00000368358 43.55 37.04 38.58 0.80 0.77 0.84 1.80 1.68 2.01
BCKDHB ENST00000320393 43.55 54.89 48.09 0.80 0.57 0.66 1.80 1.62 1.89
TCAP ENST00000309889 43.56 54.49 47.88 0.78 0.59 0.66 1.80 1.66 1.90
FAM114A1 ENST00000358869 43.56 79.52 62.39 0.78 0.38 0.48 1.80 0.66 1.41
HMGCS2 ENST00000369406 43.57 64.40 53.38 0.77 0.48 0.62 1.80 1.22 1.84
MARCH8 ENST00000395771 43.57 71.38 57.39 0.77 0.53 0.51 1.80 1.05 1.68
SLC30A6 ENST00000379343 43.58 44.83 42.47 0.77 0.68 0.68 1.80 1.97 1.99
SLC25A46 ENST00000355943 43.58 42.36 41.19 0.77 0.59 0.76 1.80 1.90 2.02
ADAMTS1 ENST00000284984 43.59 16.22 28.10 0.77 1.80 0.81 1.80 0.69 1.29
ACAT2 ENST00000367048 43.59 62.90 52.56 0.77 0.51 0.61 1.80 1.31 1.90
PDCD11 ENST00000369797 43.60 31.31 35.58 0.77 0.99 0.86 1.80 1.38 1.77
ATP1B4 ENST00000218008 43.60 48.68 44.72 0.76 0.63 0.63 1.80 1.99 2.06
TRIP10 ENST00000313285 43.61 34.21 37.17 0.76 0.84 0.81 1.79 1.56 1.97
STYXL1 ENST00000248600 43.61 75.21 59.79 0.76 0.49 0.49 1.79 0.91 1.65
XXYLT1 ENST00000310380 43.62 63.12 52.70 0.76 0.48 0.59 1.79 1.30 1.89
PCYOX1L ENST00000274569 43.62 72.77 58.26 0.76 0.48 0.47 1.79 1.04 1.65
DCBLD2 ENST00000326840 43.63 21.53 30.84 0.76 1.42 0.78 1.79 0.81 1.49
SLC22A5 ENST00000245407 43.63 71.16 57.30 0.76 0.52 0.51 1.79 1.06 1.68
ATPAF2 ENST00000474627 43.64 74.47 59.33 0.76 0.53 0.51 1.79 0.99 1.69
GABARAPL3 ENST00000412799 43.64 97.88 73.59 0.76 0.21 0.40 1.78 0.17 0.74

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