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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
AP3M1 ENST00000355264 15.63 28.89 20.32 1.57 1.15 1.47 0.77 1.30 0.88
LINGO2 ENST00000379992 15.63 21.05 16.15 1.57 1.44 1.71 0.76 0.83 0.65
CDKN2C ENST00000262662 15.64 51.23 31.64 1.57 0.65 0.89 0.76 1.90 1.58
CACNG2 ENST00000300105 15.64 16.36 13.68 1.56 1.80 2.02 0.76 0.69 0.58
SAP30BP ENST00000584667 15.65 43.36 27.65 1.56 0.59 0.95 0.76 1.95 1.27
KCNH4 ENST00000264661 15.66 7.25 8.80 1.56 2.58 2.49 0.76 0.37 0.38
DGKZ ENST00000454345 15.66 16.28 13.61 1.56 1.78 2.01 0.76 0.70 0.57
HDAC7 ENST00000080059 15.67 8.81 9.74 1.56 2.47 2.26 0.76 0.47 0.40
SCAMP3 ENST00000302631 15.67 37.60 24.67 1.56 0.80 1.05 0.77 1.69 1.10
FAM122A ENST00000394264 15.68 43.07 27.49 1.56 0.61 0.97 0.77 1.90 1.27
PCDH1 ENST00000287008 15.68 8.94 9.83 1.56 2.44 2.29 0.77 0.47 0.40
NXPH1 ENST00000405863 15.69 31.31 21.64 1.56 0.99 1.27 0.77 1.38 0.92
INO80E ENST00000563197 15.69 53.51 32.78 1.56 0.65 0.85 0.77 1.70 1.65
DDX26B ENST00000370752 15.70 3.14 6.77 1.56 3.45 2.97 0.77 0.28 0.32
CAMSAP2 ENST00000358823 15.70 4.61 7.51 1.56 3.25 2.77 0.77 0.32 0.33
SCAPER ENST00000563290 15.71 17.74 14.45 1.57 1.54 2.00 0.77 0.72 0.58
AMBRA1 ENST00000314845 15.71 2.73 6.64 1.57 3.54 3.00 0.77 0.29 0.32
SCAF8 ENST00000367178 15.72 1.09 5.67 1.57 4.03 3.35 0.77 0.28 0.27
ZBTB7C ENST00000588982 15.72 28.45 20.14 1.57 1.15 1.49 0.77 1.24 0.86
LSM14B ENST00000279068 15.73 7.69 9.12 1.57 2.52 2.37 0.77 0.42 0.38
GNA12 ENST00000275364 15.73 10.26 10.58 1.57 2.28 2.16 0.77 0.50 0.44
PCYT2 ENST00000538721 15.74 33.45 22.76 1.57 0.84 1.19 0.76 1.51 0.98
RAB4A ENST00000366690 15.74 32.36 22.19 1.57 0.87 1.15 0.77 1.46 0.96
SAMD4A ENST00000392067 15.75 6.55 8.50 1.57 2.62 2.51 0.77 0.37 0.37
ST13 ENST00000216218 15.75 20.31 15.84 1.56 1.44 1.77 0.77 0.75 0.66

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