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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
NDUFA7 ENST00000301457 76.96 91.22 87.27 0.33 0.23 0.28 0.73 0.34 0.31
TONSL ENST00000409379 76.97 36.96 56.81 0.33 0.75 0.52 0.73 1.70 1.71
PDYN ENST00000217305 76.97 86.76 85.21 0.34 0.24 0.34 0.73 0.40 0.37
SDR16C5 ENST00000303749 76.98 46.68 62.79 0.34 0.75 0.48 0.73 1.97 1.39
ARHGEF16 ENST00000378378 76.98 55.98 68.46 0.34 0.49 0.47 0.73 1.56 1.06
OR51M1 ENST00000328611 76.99 80.24 82.01 0.34 0.37 0.37 0.73 0.58 0.47
APOBEC1 ENST00000229304 76.99 83.42 83.59 0.34 0.27 0.33 0.73 0.47 0.40
UPF3A ENST00000375299 77.00 51.63 65.96 0.34 0.62 0.51 0.73 1.88 1.24
C6orf226 ENST00000408925 77.01 92.62 87.97 0.34 0.29 0.24 0.73 0.31 0.32
OR2L13 ENST00000366478 77.01 81.40 82.60 0.34 0.33 0.32 0.73 0.54 0.43
MTX1 ENST00000368376 77.02 40.66 58.95 0.34 0.63 0.49 0.73 1.77 1.65
TRIM6-TRIM34 ENST00000354852 77.02 59.86 70.77 0.34 0.52 0.43 0.72 1.36 0.86
ZSCAN31 ENST00000414429 77.03 62.09 72.22 0.34 0.56 0.43 0.72 1.36 0.82
C12orf54 ENST00000314014 77.03 80.01 81.88 0.34 0.37 0.37 0.72 0.61 0.46
FDFT1 ENST00000220584 77.04 82.57 83.19 0.34 0.34 0.29 0.72 0.51 0.40
C10orf71 ENST00000374144 77.04 43.25 60.71 0.34 0.62 0.44 0.73 1.92 1.61
DOK7 ENST00000340083 77.05 46.14 62.45 0.34 0.73 0.48 0.73 2.04 1.39
HKR1 ENST00000324411 77.05 76.91 80.30 0.34 0.43 0.38 0.73 0.79 0.52
PRM1 ENST00000312511 77.06 91.71 87.51 0.34 0.24 0.28 0.73 0.32 0.30
LAMA5 ENST00000252999 77.06 10.22 41.85 0.34 2.29 0.68 0.72 0.49 2.02
ZDBF2 ENST00000374423 77.07 22.30 48.59 0.34 1.52 0.67 0.73 0.82 1.85
ZC3H8 ENST00000409573 77.07 20.73 47.72 0.34 1.46 0.65 0.72 0.81 1.88
SRCRB4D ENST00000275560 77.08 62.38 72.46 0.34 0.53 0.44 0.72 1.33 0.83
C3orf35 ENST00000328376 77.08 86.25 85.03 0.34 0.27 0.33 0.72 0.42 0.39
SALL3 ENST00000537592 77.09 21.33 48.08 0.34 1.43 0.66 0.72 0.80 1.89

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