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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
FAM9C ENST00000333995 97.07 96.62 98.87 0.10 0.23 0.10 0.11 0.20 0.05
BTN3A1 ENST00000289361 98.39 65.76 85.44 0.10 0.54 0.34 0.10 1.22 0.35
CFHR4 ENST00000367416 97.07 72.13 87.75 0.10 0.52 0.24 0.11 1.04 0.32
FSCB ENST00000340446 98.39 97.59 99.50 0.10 0.22 0.11 0.10 0.20 0.05
ZNF728 ENST00000594710 97.06 88.33 95.46 0.10 0.23 0.08 0.11 0.37 0.11
BTN3A3 ENST00000244519 98.38 84.35 94.12 0.10 0.29 0.09 0.10 0.44 0.12
TRIM60 ENST00000512596 97.06 99.26 99.33 0.10 0.15 0.11 0.11 0.13 0.04
IBA57-AS1 ENST00000366713 98.38 98.65 99.74 0.10 0.20 0.12 0.10 0.15 0.04
PVR ENST00000425690 97.05 74.99 89.14 0.10 0.53 0.19 0.11 0.93 0.26
MS4A6A ENST00000412309 98.37 96.30 99.15 0.10 0.22 0.11 0.10 0.19 0.04
ZNF645 ENST00000323684 97.05 98.53 99.21 0.10 0.20 0.11 0.11 0.15 0.04
AADACL4 ENST00000376221 97.04 84.82 93.71 0.10 0.27 0.10 0.11 0.42 0.14
C14orf177 ENST00000325812 98.37 91.44 97.50 0.10 0.23 0.08 0.10 0.33 0.07
GNLY ENST00000263863 97.04 92.62 97.45 0.10 0.29 0.08 0.11 0.31 0.07
ZNF83 ENST00000597597 98.36 98.54 99.57 0.10 0.20 0.12 0.10 0.15 0.05
ZNF835 ENST00000537055 97.03 98.52 99.46 0.10 0.21 0.11 0.11 0.15 0.05
PAGE2B ENST00000374971 98.36 93.21 98.16 0.10 0.28 0.09 0.10 0.30 0.05
ZNF551 ENST00000282296 97.02 82.71 92.62 0.10 0.34 0.14 0.11 0.50 0.15
ZNF69 ENST00000340180 98.35 91.25 97.40 0.10 0.23 0.08 0.10 0.34 0.07
ZNF440 ENST00000304060 97.02 84.92 93.77 0.10 0.27 0.10 0.11 0.44 0.13
PRR26 ENST00000441152 98.35 45.97 75.08 0.10 0.76 0.39 0.10 2.03 0.67
DEFA5 ENST00000330590 97.01 97.18 99.04 0.10 0.24 0.11 0.11 0.19 0.04
CCDC7 ENST00000362006 97.01 53.59 78.54 0.09 0.62 0.38 0.11 1.72 0.55
KIAA1683 ENST00000392413 98.34 47.35 75.88 0.09 0.66 0.38 0.10 2.01 0.63
ZNF808 ENST00000359798 97.00 65.03 84.34 0.09 0.51 0.33 0.11 1.24 0.40

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