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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
CETN2 ENST00000370277 18.34 45.73 30.22 1.51 0.75 0.81 0.90 2.02 1.44
RCC1 ENST00000373831 18.35 15.59 14.74 1.51 1.87 1.96 0.90 0.68 0.62
PORCN ENST00000326194 18.35 2.30 7.68 1.52 3.64 2.69 0.90 0.29 0.33
ATP8B1 ENST00000536015 18.36 27.41 21.01 1.52 1.27 1.43 0.90 1.17 0.88
FNDC3B ENST00000336824 18.36 0.06 6.59 1.52 4.13 3.00 0.90 0.27 0.32
MAP3K1 ENST00000399503 18.37 5.55 9.40 1.52 2.99 2.29 0.90 0.33 0.40
TADA2B ENST00000310074 18.37 23.86 19.11 1.52 1.39 1.54 0.90 0.95 0.85
DEPDC5 ENST00000382112 18.38 14.75 14.26 1.52 1.96 2.01 0.90 0.62 0.60
RASL10B ENST00000268864 18.38 58.61 36.63 1.52 0.54 0.85 0.90 1.42 1.92
TBC1D19 ENST00000264866 18.39 26.88 20.77 1.52 1.23 1.46 0.90 1.12 0.89
NAV3 ENST00000536525 18.39 3.64 8.38 1.52 3.36 2.52 0.90 0.30 0.37
NFE2L1 ENST00000362042 18.40 7.17 10.35 1.52 2.58 2.19 0.91 0.37 0.43
BZW2 ENST00000433922 18.40 23.24 18.82 1.52 1.43 1.57 0.91 0.92 0.83
SAMD5 ENST00000367474 18.41 85.64 51.10 1.52 0.27 0.65 0.91 0.44 1.88
C17orf85 ENST00000389005 18.41 8.03 10.83 1.52 2.53 2.19 0.91 0.44 0.44
GRIPAP1 ENST00000376441 18.42 4.10 8.60 1.52 3.25 2.53 0.91 0.32 0.36
RIMS1 ENST00000521978 18.42 10.76 12.16 1.52 2.13 2.29 0.91 0.51 0.49
TAF15 ENST00000588240 18.43 18.07 16.06 1.52 1.53 1.70 0.91 0.74 0.66
TAF6 ENST00000437822 18.43 42.86 28.77 1.52 0.62 0.80 0.91 1.92 1.32
DYNC1I1 ENST00000324972 18.44 35.92 25.25 1.52 0.80 1.05 0.91 1.58 1.15
KIAA1324L ENST00000450689 18.44 27.73 21.20 1.52 1.25 1.40 0.91 1.19 0.90
ST5 ENST00000534127 18.45 6.93 10.24 1.52 2.61 2.21 0.91 0.37 0.42
TIMM17B ENST00000396779 18.45 48.32 31.62 1.52 0.63 0.89 0.91 2.01 1.57
LARGE ENST00000354992 18.46 12.12 12.82 1.52 2.07 2.11 0.91 0.57 0.52
ARL5B ENST00000377275 18.46 51.21 32.98 1.53 0.65 0.85 0.91 1.91 1.67

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