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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
SIX1 ENST00000247182 19.37 25.89 20.78 1.56 1.21 1.47 0.98 1.08 0.88
CACNA1F ENST00000376265 19.38 20.54 17.89 1.56 1.44 1.68 0.97 0.78 0.77
UQCRFS1 ENST00000304863 19.38 40.22 27.97 1.56 0.61 0.82 0.97 1.72 1.27
WNT2B ENST00000369684 19.39 32.72 24.07 1.56 0.84 1.10 0.97 1.45 1.06
JAG2 ENST00000331782 19.39 2.45 8.28 1.56 3.58 2.57 0.98 0.29 0.37
CACNG4 ENST00000262138 19.40 42.96 29.37 1.54 0.62 0.82 0.98 1.90 1.36
FAM188A ENST00000277632 19.40 20.06 17.61 1.54 1.43 1.64 0.98 0.74 0.77
KCTD13 ENST00000568000 19.41 51.68 33.72 1.54 0.61 0.89 0.98 1.87 1.73
STXBP3 ENST00000370008 19.42 31.50 23.55 1.54 0.96 1.19 0.98 1.43 1.01
SLC1A5 ENST00000542575 19.42 31.57 23.61 1.56 0.94 1.19 0.98 1.44 1.02
PLAA ENST00000397292 19.43 18.05 16.57 1.57 1.53 1.72 0.98 0.74 0.70
DTL ENST00000366991 19.43 25.28 20.46 1.57 1.28 1.49 0.98 1.02 0.89
PCBP3 ENST00000400314 19.44 17.35 16.21 1.57 1.61 1.71 0.98 0.75 0.66
COPZ1 ENST00000262061 19.44 14.93 14.97 1.57 1.94 1.89 0.98 0.63 0.63
RALGAPA1 ENST00000307138 19.45 8.19 11.49 1.58 2.57 2.19 0.98 0.44 0.45
SNCB ENST00000310112 19.45 56.89 36.29 1.58 0.56 0.85 0.98 1.54 1.86
DOCK4 ENST00000437633 19.46 11.14 12.86 1.58 2.09 2.11 0.98 0.54 0.53
RNF14 ENST00000394520 19.46 35.92 25.80 1.58 0.80 1.01 0.98 1.58 1.23
CCND3 ENST00000372991 19.47 10.11 12.37 1.57 2.33 2.23 0.98 0.48 0.50
ZNF449 ENST00000339249 19.47 21.89 18.67 1.57 1.46 1.58 0.99 0.81 0.81
FAM46C ENST00000369448 19.48 13.80 14.36 1.57 2.06 2.01 0.99 0.60 0.59
TFAM ENST00000487519 19.48 30.72 23.20 1.57 1.05 1.19 0.99 1.37 1.02
RAB3C ENST00000282878 19.49 65.51 40.66 1.57 0.53 0.81 0.99 1.23 2.05
WDR37 ENST00000358220 19.49 19.93 17.55 1.57 1.44 1.63 0.99 0.73 0.75
DGKD ENST00000264057 19.50 15.76 15.41 1.57 1.87 1.81 0.99 0.69 0.67

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