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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
TBCK ENST00000273980 42.10 47.16 42.96 0.78 0.66 0.67 1.75 1.99 2.00
PHLDB2 ENST00000431670 42.11 30.80 34.69 0.78 1.06 0.90 1.75 1.37 1.75
P2RX7 ENST00000546057 42.11 50.34 44.87 0.78 0.66 0.68 1.75 1.97 2.04
BCAN ENST00000329117 42.12 32.38 35.44 0.78 0.87 0.87 1.75 1.47 1.77
SFRP5 ENST00000266066 42.12 76.36 59.56 0.80 0.43 0.49 1.75 0.86 1.69
PRMT3 ENST00000331079 42.13 79.59 61.58 0.78 0.38 0.46 1.75 0.66 1.48
CBX6 ENST00000407418 42.13 10.30 24.22 0.78 2.28 1.13 1.75 0.49 1.05
GFOD2 ENST00000268797 42.14 43.15 40.82 0.78 0.62 0.80 1.75 1.90 2.04
GPR156 ENST00000464295 42.14 57.05 48.46 0.78 0.56 0.68 1.74 1.51 1.87
MKL1 ENST00000355630 42.15 9.50 23.86 0.78 2.49 1.09 1.74 0.49 1.04
DYSF ENST00000410020 42.15 38.75 38.71 0.78 0.70 0.82 1.74 1.67 2.02
RAD1 ENST00000382038 42.16 61.83 51.09 0.78 0.57 0.65 1.74 1.36 1.88
SHC3 ENST00000375835 42.16 27.16 32.83 0.78 1.24 0.85 1.74 1.14 1.65
BVES ENST00000314641 42.17 54.09 46.84 0.78 0.65 0.67 1.74 1.68 1.88
UNC13C ENST00000260323 42.17 26.41 32.52 0.78 1.16 0.89 1.74 1.09 1.61
CRYBG3 ENST00000182096 42.18 23.07 30.85 0.78 1.46 0.77 1.74 0.91 1.49
DMD ENST00000357033 42.18 3.35 20.90 0.78 3.44 1.44 1.74 0.28 0.87
PARP14 ENST00000474629 42.19 16.11 27.29 0.78 1.82 0.97 1.75 0.69 1.24
MRPL19 ENST00000393909 42.19 38.84 38.81 0.78 0.68 0.82 1.75 1.66 2.03
LAMB1 ENST00000222399 42.20 32.50 35.51 0.78 0.86 0.85 1.75 1.48 1.78
TMEM219 ENST00000566848 42.20 77.54 60.35 0.78 0.42 0.46 1.75 0.79 1.58
HBG2 ENST00000380259 42.21 50.49 45.00 0.78 0.65 0.70 1.75 1.94 2.04
CCSER1 ENST00000509176 42.21 28.37 33.44 0.78 1.16 0.89 1.75 1.22 1.70
FANCD2OS ENST00000450660 42.22 75.66 59.11 0.78 0.44 0.49 1.75 0.90 1.68
CHPT1 ENST00000229266 42.22 44.67 41.66 0.78 0.66 0.72 1.75 1.98 2.01

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