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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
C5orf63 ENST00000535381 91.13 94.50 95.79 0.15 0.23 0.07 0.21 0.24 0.11
C13orf45 ENST00000318245 93.47 96.25 95.79 0.13 0.22 0.07 0.15 0.19 0.11
NME3 ENST00000219302 92.56 94.72 95.80 0.15 0.23 0.07 0.18 0.24 0.11
ZNF559 ENST00000393883 95.21 90.91 95.80 0.10 0.25 0.07 0.12 0.35 0.11
VCX2 ENST00000317103 89.74 96.31 95.81 0.16 0.22 0.07 0.28 0.19 0.11
SPANXC ENST00000358993 90.56 95.23 95.81 0.16 0.23 0.07 0.24 0.21 0.11
C14orf144 ENST00000419115 91.15 94.53 95.82 0.15 0.23 0.07 0.21 0.24 0.11
MBD3L4 ENST00000381394 89.89 93.44 95.82 0.16 0.28 0.07 0.28 0.28 0.11
RP11-297N6.4 ENST00000533405 92.33 96.20 95.83 0.15 0.22 0.07 0.18 0.20 0.11
GRIK1-AS2 ENST00000333765 87.55 98.42 95.83 0.23 0.21 0.07 0.37 0.14 0.11
PRAMEF15 ENST00000330087 93.85 92.01 95.84 0.11 0.24 0.07 0.13 0.33 0.11
PRR4 ENST00000228811 99.12 87.10 95.84 0.11 0.22 0.07 0.12 0.41 0.11
BHLHA9 ENST00000391429 92.63 93.29 95.85 0.15 0.28 0.07 0.18 0.30 0.11
TREML4 ENST00000341495 98.79 87.44 95.85 0.10 0.23 0.07 0.11 0.40 0.11
PSG6 ENST00000292125 95.00 91.23 95.86 0.10 0.23 0.07 0.12 0.34 0.11
PSORS1C1 ENST00000259881 94.33 91.93 95.86 0.10 0.23 0.07 0.11 0.33 0.11
TMEM99 ENST00000301665 88.30 97.87 95.87 0.20 0.21 0.07 0.35 0.17 0.11
RP11-467N20.5 ENST00000558241 89.08 97.19 95.87 0.19 0.24 0.07 0.32 0.19 0.11
EDDM3A ENST00000326842 86.76 99.44 95.88 0.24 0.16 0.07 0.40 0.12 0.11
TMEM61 ENST00000371268 95.65 90.66 95.88 0.11 0.25 0.07 0.11 0.36 0.11
C12orf61 ENST00000408887 88.08 98.09 95.89 0.20 0.20 0.07 0.35 0.16 0.11
OR11H12 ENST00000550708 88.73 97.57 95.89 0.19 0.22 0.07 0.33 0.20 0.11
RP13-996F3.4 ENST00000557886 90.33 95.74 95.90 0.15 0.23 0.07 0.25 0.20 0.10
DCAF4L2 ENST00000319675 86.66 99.61 95.90 0.24 0.16 0.07 0.41 0.12 0.10
CT45A6 ENST00000491002 93.00 93.08 95.91 0.16 0.28 0.07 0.15 0.30 0.10

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