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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
ANP32D ENST00000266594 96.26 98.46 99.24 0.12 0.21 0.11 0.11 0.14 0.04
FP15737 ENST00000399967 91.41 98.40 97.79 0.15 0.21 0.09 0.20 0.14 0.04
AL590822.1 ENST00000545087 91.42 98.40 97.80 0.15 0.21 0.09 0.20 0.14 0.04
ARMS2 ENST00000528446 98.33 96.64 99.24 0.09 0.23 0.11 0.10 0.20 0.04
ZG16B ENST00000382280 99.46 91.04 97.80 0.11 0.25 0.09 0.13 0.36 0.04
C22orf29 ENST00000405640 95.55 99.32 99.25 0.11 0.16 0.11 0.11 0.12 0.04
NBPF15 ENST00000442702 94.36 96.15 97.81 0.10 0.21 0.09 0.11 0.20 0.04
C15orf37 ENST00000560255 95.17 99.78 99.25 0.10 0.17 0.11 0.12 0.11 0.04
USP17L5 ENST00000507227 91.46 98.43 97.82 0.15 0.21 0.09 0.20 0.14 0.04
IFNA16 ENST00000380216 95.63 98.74 99.26 0.11 0.16 0.11 0.11 0.14 0.04
SPATA31A7 ENST00000355045 90.24 96.43 97.82 0.16 0.22 0.09 0.26 0.19 0.04
DEFB125 ENST00000382410 99.24 95.82 99.26 0.11 0.22 0.11 0.12 0.20 0.04
ZNF284 ENST00000421176 99.31 91.26 97.83 0.11 0.23 0.09 0.12 0.34 0.04
OR6F1 ENST00000302084 94.74 95.84 97.83 0.10 0.22 0.09 0.11 0.20 0.04
DPRX ENST00000376650 98.80 96.33 99.27 0.10 0.22 0.11 0.11 0.19 0.04
SPATA31A6 ENST00000332857 95.50 95.07 97.84 0.11 0.23 0.09 0.11 0.21 0.04
OR2M3 ENST00000456743 97.30 97.77 99.27 0.10 0.21 0.11 0.11 0.17 0.04
AL627171.2 ENST00000595378 91.48 98.45 97.84 0.15 0.21 0.09 0.20 0.14 0.04
FAM220A ENST00000313324 95.87 99.14 99.28 0.11 0.15 0.11 0.11 0.14 0.04
ERVV-1 ENST00000602168 92.29 98.88 97.85 0.15 0.17 0.09 0.19 0.14 0.04
AP001816.1 ENST00000527564 92.48 99.01 97.85 0.15 0.15 0.09 0.18 0.15 0.04
MRGPRD ENST00000309106 97.55 97.59 99.28 0.10 0.22 0.11 0.11 0.20 0.04
SELV ENST00000335426 95.75 94.83 97.86 0.11 0.23 0.09 0.12 0.24 0.04
KRTAP13-1 ENST00000355459 96.13 98.88 99.29 0.11 0.17 0.11 0.11 0.14 0.04
CASC10 ENST00000377113 96.38 94.30 97.86 0.10 0.24 0.09 0.11 0.25 0.04

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