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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
TMPRSS12 ENST00000398458 84.45 66.91 78.98 0.30 0.53 0.39 0.46 1.25 0.53
CA5A ENST00000309893 84.46 52.37 70.76 0.30 0.62 0.43 0.46 1.82 0.86
MT1HL1 ENST00000464121 84.46 98.42 94.33 0.30 0.21 0.10 0.46 0.14 0.12
GPR135 ENST00000395116 84.47 79.54 85.36 0.30 0.38 0.34 0.46 0.66 0.36
FREM3 ENST00000329798 84.47 47.65 68.01 0.30 0.61 0.51 0.46 1.97 1.10
RP11-723O4.6 ENST00000508239 84.48 68.40 79.74 0.30 0.52 0.38 0.46 1.21 0.53
C19orf73 ENST00000408991 84.48 94.73 92.29 0.30 0.23 0.14 0.46 0.24 0.15
GIMAP5 ENST00000358647 84.49 92.78 91.50 0.30 0.29 0.15 0.46 0.30 0.18
HIST3H3 ENST00000366696 84.49 96.06 93.03 0.30 0.21 0.14 0.46 0.20 0.15
KLRC4 ENST00000309384 84.50 77.28 84.16 0.30 0.42 0.34 0.46 0.77 0.42
RNASE11 ENST00000610205 84.50 99.72 94.91 0.30 0.17 0.09 0.46 0.11 0.11
KIAA0226L ENST00000429979 84.51 70.32 80.73 0.30 0.52 0.39 0.46 1.10 0.52
UGT2B15 ENST00000338206 84.52 88.54 89.66 0.30 0.24 0.18 0.46 0.36 0.23
ZNF839 ENST00000442396 84.52 42.11 64.67 0.30 0.61 0.51 0.46 1.86 1.32
ZNF792 ENST00000404801 84.53 71.43 81.34 0.30 0.53 0.38 0.46 1.06 0.49
OXLD1 ENST00000374741 84.53 79.91 85.59 0.29 0.37 0.32 0.46 0.61 0.35
C12orf60 ENST00000330828 84.54 86.14 88.47 0.29 0.27 0.22 0.46 0.42 0.29
C1orf100 ENST00000308105 84.54 79.20 85.23 0.29 0.39 0.34 0.46 0.69 0.36
TSFM ENST00000323833 84.55 68.91 80.06 0.29 0.54 0.35 0.46 1.16 0.52
C19orf25 ENST00000436106 84.55 86.33 88.56 0.29 0.25 0.22 0.46 0.43 0.28
IL6R ENST00000368485 84.56 44.30 66.08 0.29 0.61 0.51 0.46 1.95 1.23
CXCL6 ENST00000226317 84.56 97.27 93.68 0.29 0.23 0.11 0.46 0.19 0.14
C1orf68 ENST00000368775 84.57 85.26 88.07 0.29 0.25 0.23 0.46 0.46 0.30
SULT1C3 ENST00000329106 84.57 95.59 92.84 0.29 0.23 0.14 0.46 0.21 0.15
NDUFA4L2 ENST00000393825 84.58 79.40 85.33 0.29 0.38 0.34 0.46 0.67 0.36

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