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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
RHOT2 ENST00000315082 78.64 76.12 80.70 0.35 0.43 0.39 0.65 0.86 0.52
OR4D9 ENST00000329328 78.65 83.00 84.08 0.35 0.32 0.35 0.65 0.49 0.42
OR5M9 ENST00000279791 78.65 82.64 83.95 0.35 0.34 0.35 0.65 0.50 0.43
OPLAH ENST00000426825 78.66 41.75 60.80 0.35 0.61 0.43 0.65 1.78 1.60
SGK223 ENST00000520004 78.66 77.71 81.54 0.35 0.42 0.35 0.64 0.79 0.48
ROGDI ENST00000322048 78.67 75.97 80.64 0.35 0.43 0.39 0.64 0.86 0.51
PCDHB7 ENST00000231137 78.67 88.63 86.80 0.35 0.24 0.29 0.64 0.35 0.32
ZNF771 ENST00000319296 78.68 57.55 70.41 0.35 0.57 0.43 0.64 1.48 0.91
ERMARD ENST00000366773 78.68 56.80 69.94 0.35 0.54 0.47 0.64 1.54 0.92
GLTSCR2 ENST00000246802 78.69 22.63 49.59 0.35 1.47 0.67 0.64 0.86 1.84
SLC25A26 ENST00000354883 78.69 65.80 75.17 0.35 0.54 0.38 0.64 1.22 0.67
CLEC7A ENST00000304084 78.70 92.69 88.79 0.35 0.29 0.19 0.65 0.30 0.28
DOHH ENST00000427575 78.70 52.86 67.61 0.35 0.65 0.51 0.65 1.80 1.12
MRPL21 ENST00000362034 78.71 91.49 88.29 0.35 0.23 0.22 0.65 0.32 0.30
OR2A7 ENST00000493325 78.71 56.64 69.91 0.35 0.53 0.46 0.65 1.55 0.92
OR4K15 ENST00000305051 78.72 78.04 81.75 0.35 0.42 0.35 0.65 0.76 0.47
ENPP7 ENST00000328313 78.73 89.52 87.31 0.35 0.27 0.28 0.65 0.36 0.31
SHISA6 ENST00000441885 78.73 19.12 47.74 0.35 1.49 0.65 0.65 0.76 1.88
AGPAT5 ENST00000285518 78.74 46.49 63.88 0.35 0.73 0.49 0.65 2.02 1.39
HRG ENST00000232003 78.74 78.07 81.78 0.35 0.43 0.37 0.65 0.75 0.47
IRAK2 ENST00000256458 78.75 67.61 76.27 0.35 0.53 0.37 0.65 1.19 0.61
HPS4 ENST00000398145 78.75 33.58 55.84 0.35 0.85 0.51 0.65 1.54 1.75
NUSAP1 ENST00000559596 78.76 27.69 52.53 0.35 1.27 0.61 0.65 1.19 1.90
DGCR6L ENST00000248879 78.76 70.04 77.61 0.35 0.53 0.38 0.65 1.14 0.56
APRT ENST00000378364 78.77 96.92 90.89 0.35 0.23 0.15 0.65 0.19 0.20

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