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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
ILDR1 ENST00000344209 52.82 58.91 55.52 0.66 0.53 0.52 1.78 1.42 1.74
TMEM119 ENST00000392806 52.82 53.13 52.19 0.66 0.66 0.61 1.77 1.77 1.89
MYCBP ENST00000397572 52.83 24.35 36.76 0.66 1.32 0.82 1.77 1.00 1.94
ULK1 ENST00000321867 52.83 11.34 30.27 0.66 2.11 0.84 1.77 0.56 1.44
CISH ENST00000443053 52.84 67.68 60.89 0.66 0.53 0.43 1.77 1.19 1.59
RWDD2B ENST00000493196 52.84 74.79 65.24 0.66 0.53 0.53 1.77 0.96 1.31
ZCCHC4 ENST00000302874 52.85 52.42 51.78 0.66 0.63 0.62 1.77 1.83 1.93
SAMD1 ENST00000533683 52.85 36.24 42.85 0.66 0.82 0.68 1.77 1.61 2.01
ARMCX5 ENST00000604957 52.86 46.51 48.59 0.66 0.73 0.67 1.77 2.02 1.85
NARS2 ENST00000281038 52.86 46.09 48.34 0.66 0.75 0.67 1.77 2.03 1.88
KIF14 ENST00000367350 52.87 20.02 34.69 0.65 1.43 0.90 1.77 0.73 1.75
ANLN ENST00000265748 52.87 15.71 32.47 0.65 1.87 0.90 1.77 0.68 1.63
KIAA1549L ENST00000321505 52.88 23.78 36.42 0.63 1.38 0.84 1.78 0.93 1.87
TTLL9 ENST00000375938 52.88 71.66 63.44 0.63 0.53 0.51 1.78 1.07 1.38
MMP27 ENST00000260229 52.89 85.10 71.51 0.65 0.25 0.44 1.78 0.45 0.84
HERC5 ENST00000264350 52.89 34.70 42.02 0.65 0.80 0.70 1.78 1.54 1.99
GLB1L ENST00000295759 52.90 53.80 52.68 0.65 0.63 0.59 1.78 1.70 1.89
NEFH ENST00000310624 52.91 56.08 53.98 0.65 0.51 0.61 1.78 1.56 1.77
COASY ENST00000590958 52.91 59.95 56.16 0.65 0.53 0.49 1.78 1.37 1.77
ENPP6 ENST00000296741 52.92 67.57 60.84 0.65 0.53 0.43 1.78 1.20 1.61
ZCCHC2 ENST00000269499 52.92 11.72 30.57 0.65 2.07 0.80 1.77 0.57 1.47
MRC1L1 ENST00000331429 52.93 9.60 29.44 0.65 2.48 0.85 1.77 0.50 1.36
ROR2 ENST00000375708 52.93 26.46 37.97 0.65 1.16 0.85 1.77 1.10 2.02
RANBP3L ENST00000502994 52.94 65.64 59.60 0.65 0.53 0.49 1.77 1.21 1.69
PIGW ENST00000592983 52.94 56.83 54.44 0.65 0.56 0.57 1.76 1.54 1.75

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