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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
CLN6 ENST00000249806 42.62 61.95 51.41 0.76 0.56 0.63 1.77 1.36 1.90
MYLK2 ENST00000375994 42.62 23.67 31.37 0.76 1.40 0.87 1.77 0.93 1.55
BRSK2 ENST00000382179 42.63 14.21 26.51 0.76 2.06 0.99 1.77 0.60 1.25
ADPRH ENST00000478399 42.63 70.43 56.29 0.76 0.52 0.49 1.77 1.08 1.75
PDIA5 ENST00000316218 42.64 43.79 41.44 0.76 0.61 0.73 1.78 1.96 2.02
LAP3 ENST00000226299 42.64 49.53 44.61 0.76 0.66 0.62 1.78 2.04 2.05
NDUFB5 ENST00000259037 42.65 63.60 52.38 0.76 0.51 0.61 1.77 1.24 1.90
UQCRQ ENST00000378670 42.65 85.51 65.69 0.76 0.27 0.51 1.77 0.45 1.27
CENPL ENST00000356198 42.66 30.53 34.78 0.76 1.09 0.90 1.77 1.38 1.77
STARD10 ENST00000334805 42.66 53.12 46.59 0.77 0.66 0.66 1.77 1.77 1.89
FAT2 ENST00000261800 42.67 26.08 32.59 0.77 1.20 0.87 1.78 1.09 1.63
AIG1 ENST00000357847 42.67 75.74 59.49 0.77 0.44 0.49 1.78 0.88 1.70
CTGF ENST00000367976 42.68 52.63 46.29 0.77 0.68 0.67 1.78 1.81 1.92
GPATCH2 ENST00000366935 42.68 56.43 48.42 0.78 0.52 0.67 1.78 1.53 1.87
CXorf57 ENST00000372548 42.69 33.85 36.37 0.78 0.85 0.85 1.78 1.56 1.87
BSDC1 ENST00000446293 42.69 30.22 34.70 0.78 1.09 0.90 1.78 1.41 1.76
PRC1 ENST00000394249 42.70 32.19 35.57 0.78 0.86 0.86 1.78 1.46 1.78
KIAA1715 ENST00000272748 42.70 34.36 36.72 0.78 0.82 0.82 1.78 1.56 1.94
NDUFA5 ENST00000355749 42.71 74.28 58.60 0.78 0.53 0.51 1.78 1.01 1.65
FMO5 ENST00000254090 42.71 78.38 61.16 0.78 0.43 0.43 1.78 0.74 1.51
CLDND1 ENST00000437922 42.72 32.09 35.54 0.78 0.91 0.85 1.77 1.46 1.78
THG1L ENST00000231198 42.73 55.68 48.06 0.78 0.52 0.67 1.77 1.60 1.88
MUL1 ENST00000264198 42.73 64.34 52.84 0.78 0.49 0.61 1.77 1.21 1.88
FEM1A ENST00000269856 42.74 75.00 58.98 0.78 0.53 0.49 1.77 0.93 1.65
THAP2 ENST00000308086 42.74 87.09 66.61 0.78 0.22 0.52 1.77 0.40 1.20

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