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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
CDK13 ENST00000181839 8.91 12.83 8.20 2.35 2.09 2.57 0.45 0.59 0.37
SNRNP27 ENST00000244227 8.92 59.88 32.61 2.35 0.53 0.87 0.45 1.36 1.63
PRKCI ENST00000295797 8.93 19.45 11.80 2.35 1.44 2.21 0.45 0.74 0.46
RPL24 ENST00000394077 8.93 25.99 15.23 2.35 1.20 1.83 0.45 1.10 0.65
CHERP ENST00000546361 8.94 0.32 2.31 2.35 4.14 4.03 0.45 0.28 0.22
ADCY1 ENST00000297323 8.94 10.57 7.11 2.35 2.15 2.87 0.45 0.52 0.33
FUS ENST00000254108 8.95 7.63 5.60 2.35 2.49 3.39 0.45 0.42 0.27
MED15 ENST00000263205 8.95 8.76 6.12 2.35 2.47 3.24 0.45 0.48 0.30
RGS8 ENST00000258302 8.96 32.05 18.44 2.34 0.92 1.62 0.45 1.47 0.81
SMURF2 ENST00000262435 8.96 14.50 9.18 2.34 2.02 2.32 0.45 0.61 0.38
BTBD3 ENST00000405977 8.97 24.20 14.29 2.34 1.33 2.01 0.45 0.99 0.60
RAB12 ENST00000329286 8.97 37.03 21.14 2.33 0.77 1.42 0.45 1.68 0.90
STK24 ENST00000376547 8.98 23.93 14.18 2.33 1.38 1.99 0.45 0.95 0.60
POT1 ENST00000357628 8.98 16.65 10.40 2.33 1.73 2.19 0.46 0.71 0.43
UBQLN4 ENST00000368309 8.99 13.36 8.52 2.33 2.04 2.51 0.46 0.60 0.37
DTX3 ENST00000548198 8.99 19.90 12.03 2.33 1.43 2.29 0.46 0.73 0.47
ATRNL1 ENST00000355044 9.00 10.03 6.87 2.33 2.35 2.92 0.46 0.49 0.33
C7orf55-LUC7L2 ENST00000354926 9.00 25.58 15.09 2.33 1.25 1.86 0.46 1.05 0.62
CDC40 ENST00000368932 9.01 12.75 8.24 2.33 2.09 2.58 0.46 0.59 0.37
AFG3L2 ENST00000269143 9.01 36.24 20.79 2.33 0.82 1.47 0.46 1.61 0.88
ASAP1 ENST00000357668 9.02 5.36 4.47 2.33 3.07 3.70 0.46 0.32 0.25
SOGA3 ENST00000556132 9.02 15.55 9.82 2.33 1.87 2.29 0.46 0.67 0.40
UBP1 ENST00000283629 9.03 0.74 2.49 2.33 4.10 4.02 0.46 0.27 0.24
ATG5 ENST00000369076 9.03 12.91 8.34 2.33 2.07 2.53 0.46 0.59 0.37
TBC1D25 ENST00000376771 9.04 25.28 14.92 2.33 1.29 1.91 0.46 1.02 0.63

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