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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
TBC1D22B ENST00000373491 19.50 22.60 19.05 1.57 1.48 1.54 0.99 0.86 0.85
MBOAT2 ENST00000305997 19.51 20.38 17.86 1.57 1.43 1.67 1.00 0.76 0.77
ZNF821 ENST00000425432 19.51 37.71 26.78 1.57 0.78 0.96 1.00 1.70 1.27
PRR12 ENST00000418929 19.52 0.11 7.18 1.57 4.11 2.86 0.99 0.28 0.34
TMEM110 ENST00000355083 19.52 30.09 22.98 1.57 1.08 1.20 1.00 1.41 0.98
NTN4 ENST00000343702 19.53 13.63 14.31 1.57 2.05 2.00 1.00 0.59 0.60
TCF7 ENST00000342854 19.53 33.40 24.53 1.57 0.84 1.06 1.00 1.51 1.08
CRLF3 ENST00000324238 19.54 34.85 25.27 1.56 0.76 1.05 1.00 1.55 1.15
MBD1 ENST00000590208 19.54 10.54 12.59 1.57 2.18 2.20 1.00 0.51 0.52
KPNA5 ENST00000368564 19.55 31.66 23.71 1.57 0.94 1.15 1.01 1.45 1.02
MGST3 ENST00000367889 19.55 71.73 44.06 1.57 0.51 0.61 1.01 1.07 2.02
RBMS3 ENST00000383767 19.56 21.92 18.76 1.57 1.46 1.57 1.01 0.81 0.82
AMMECR1 ENST00000262844 19.57 23.12 19.35 1.57 1.46 1.54 1.01 0.91 0.85
ZEB1 ENST00000361642 19.57 13.52 14.25 1.56 2.07 2.01 1.01 0.61 0.60
KCNK5 ENST00000359534 19.58 28.12 21.97 1.56 1.19 1.19 1.00 1.20 0.96
ALDOC ENST00000226253 19.58 32.79 24.21 1.56 0.84 1.11 1.00 1.44 1.05
NFKBIA ENST00000216797 19.59 5.92 10.31 1.56 2.82 2.19 1.00 0.35 0.42
PRCC ENST00000271526 19.59 14.44 14.79 1.56 2.04 1.95 1.00 0.61 0.62
MAGED1 ENST00000375695 19.60 8.06 11.49 1.56 2.53 2.19 1.00 0.44 0.45
OSBPL6 ENST00000392505 19.60 6.09 10.42 1.56 2.78 2.18 1.00 0.35 0.43
CHRM5 ENST00000383263 19.61 41.27 28.59 1.56 0.61 0.80 1.00 1.82 1.35
TMTC3 ENST00000266712 19.61 27.75 21.83 1.56 1.25 1.23 1.01 1.19 0.95
KIAA0100 ENST00000528896 19.62 20.25 17.83 1.56 1.43 1.68 1.01 0.75 0.77
INTS2 ENST00000444766 19.62 10.83 12.77 1.56 2.14 2.13 1.01 0.50 0.52
WBP1L ENST00000448841 19.63 25.31 20.59 1.56 1.28 1.48 1.01 1.03 0.88

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