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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
FBXO47 ENST00000378079 35.00 26.37 28.83 0.92 1.18 0.80 1.86 1.08 1.31
CHST3 ENST00000373115 35.00 41.43 36.32 0.92 0.62 0.85 1.86 1.81 1.87
TCF7L1 ENST00000282111 35.01 21.68 26.43 0.92 1.46 1.01 1.87 0.81 1.25
LGI4 ENST00000310123 35.01 35.76 33.54 0.92 0.78 0.87 1.87 1.58 1.72
RAB13 ENST00000368575 35.02 40.38 35.79 0.92 0.61 0.85 1.87 1.76 1.78
ABHD6 ENST00000478253 35.02 53.73 42.66 0.92 0.63 0.68 1.87 1.70 2.02
KIAA2026 ENST00000399933 35.03 15.23 23.21 0.92 1.89 1.19 1.87 0.67 1.01
DOK4 ENST00000340099 35.03 31.09 31.28 0.92 1.02 0.86 1.87 1.36 1.55
ENO1 ENST00000234590 35.04 47.59 39.68 0.92 0.61 0.80 1.87 2.00 2.04
SKIV2L ENST00000375394 35.04 47.60 39.65 0.92 0.62 0.80 1.87 1.99 2.05
BRINP3 ENST00000367462 35.05 22.27 26.80 0.92 1.53 0.96 1.87 0.83 1.28
TTN ENST00000589042 35.06 14.95 23.10 0.92 1.92 1.20 1.87 0.62 1.00
CARF ENST00000402905 35.06 36.89 34.19 0.92 0.76 0.87 1.87 1.70 1.75
RBL2 ENST00000262133 35.07 8.93 20.05 0.92 2.44 1.49 1.87 0.48 0.85
LANCL2 ENST00000254770 35.07 24.38 27.88 0.92 1.30 0.85 1.87 1.00 1.29
PHGDH ENST00000369409 35.08 41.84 36.58 0.92 0.61 0.85 1.87 1.80 1.91
MYD88 ENST00000417037 35.08 33.55 32.51 0.94 0.85 0.89 1.86 1.53 1.62
BRD2 ENST00000395289 35.09 6.80 18.93 0.94 2.64 1.54 1.85 0.37 0.83
ATP13A4 ENST00000342695 35.09 49.95 40.68 0.94 0.66 0.81 1.85 2.02 2.04
SEC23IP ENST00000369075 35.10 26.44 28.92 0.92 1.16 0.81 1.85 1.10 1.31
FKTN ENST00000223528 35.10 45.99 38.86 0.92 0.77 0.80 1.85 2.02 2.05
IGFBP5 ENST00000233813 35.11 12.04 21.72 0.92 2.06 1.25 1.85 0.57 0.93
SRPR ENST00000332118 35.11 12.45 21.91 0.92 2.06 1.18 1.85 0.59 0.96
BLOC1S6 ENST00000220531 35.12 85.74 61.05 0.92 0.27 0.43 1.86 0.44 1.55
B3GNT7 ENST00000287590 35.12 24.44 27.94 0.92 1.32 0.84 1.86 1.00 1.28

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