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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
ZSCAN5B ENST00000586855 97.62 92.68 97.73 0.10 0.29 0.09 0.11 0.30 0.05
C17orf72 ENST00000425164 97.63 71.31 87.63 0.10 0.53 0.25 0.11 1.07 0.31
SLC22A18AS ENST00000533594 97.63 87.58 95.33 0.10 0.23 0.08 0.11 0.37 0.10
ZNF337 ENST00000376436 97.64 83.66 93.37 0.10 0.27 0.11 0.10 0.47 0.15
ORM2 ENST00000431067 97.64 75.80 89.81 0.10 0.43 0.18 0.10 0.88 0.23
BTNL8 ENST00000340184 97.65 58.03 81.18 0.10 0.53 0.38 0.10 1.45 0.49
PLIN4 ENST00000301286 97.66 80.51 91.84 0.10 0.37 0.14 0.10 0.58 0.17
ZNF225 ENST00000262894 97.66 67.19 85.74 0.10 0.54 0.33 0.10 1.22 0.33
ZNF763 ENST00000590798 97.67 76.99 90.37 0.10 0.43 0.15 0.10 0.79 0.21
AIM2 ENST00000368130 97.67 84.24 93.76 0.10 0.28 0.10 0.10 0.44 0.13
RFPL1 ENST00000354373 97.68 87.62 95.40 0.10 0.23 0.08 0.10 0.35 0.11
ZNF57 ENST00000306908 97.68 81.36 92.21 0.10 0.33 0.14 0.10 0.54 0.16
C19orf18 ENST00000314391 97.69 83.64 93.38 0.10 0.27 0.11 0.10 0.47 0.15
SLC22A14 ENST00000273173 97.69 69.72 86.87 0.10 0.53 0.29 0.10 1.13 0.31
C1orf170 ENST00000433179 97.70 86.60 94.91 0.10 0.24 0.09 0.10 0.40 0.11
PALM3 ENST00000340790 97.70 32.49 66.83 0.10 0.86 0.53 0.10 1.48 1.20
H1FOO ENST00000324382 97.71 52.73 78.46 0.10 0.66 0.38 0.10 1.79 0.54
GCSAML ENST00000366488 97.71 63.98 84.11 0.10 0.48 0.34 0.10 1.20 0.42
TCP10 ENST00000397829 97.72 67.95 86.07 0.10 0.52 0.33 0.10 1.17 0.33
XAGE3 ENST00000346279 97.72 71.75 87.86 0.10 0.51 0.24 0.10 1.07 0.32
ZNF534 ENST00000332323 97.73 93.97 98.19 0.10 0.25 0.09 0.10 0.26 0.05
AP000350.4 ENST00000406213 97.73 86.18 94.70 0.10 0.27 0.09 0.10 0.42 0.11
CEACAM21 ENST00000401445 97.74 86.08 94.64 0.10 0.27 0.09 0.10 0.44 0.11
ZNF766 ENST00000439461 97.74 90.02 96.67 0.10 0.25 0.08 0.10 0.37 0.08
CD33 ENST00000262262 97.75 71.72 87.85 0.10 0.51 0.24 0.10 1.07 0.32

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