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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
GPX7 ENST00000361314 36.03 75.13 55.17 0.94 0.51 0.51 1.85 0.91 1.74
GDF6 ENST00000287020 36.04 7.40 19.77 0.94 2.53 1.49 1.85 0.39 0.85
GOLGA1 ENST00000373555 36.04 27.94 30.17 0.94 1.20 0.81 1.85 1.19 1.45
LRRC36 ENST00000329956 36.05 50.13 41.33 0.94 0.67 0.73 1.85 1.99 2.02
LPAR2 ENST00000542587 36.05 44.92 38.78 0.94 0.68 0.82 1.85 1.98 2.03
PEX6 ENST00000304611 36.06 31.41 31.95 0.94 0.96 0.91 1.85 1.42 1.58
COX15 ENST00000016171 36.06 70.22 52.41 0.94 0.52 0.61 1.84 1.12 1.91
FGFR1OP2 ENST00000229395 36.07 46.34 39.57 0.94 0.73 0.80 1.84 2.05 2.03
FUCA1 ENST00000374479 36.07 51.72 42.14 0.94 0.61 0.70 1.84 1.88 2.01
TTC21B ENST00000243344 36.08 43.88 38.28 0.94 0.61 0.85 1.84 1.96 2.04
KRTAP17-1 ENST00000334202 36.08 55.90 44.53 0.94 0.51 0.62 1.84 1.56 2.04
DOK5 ENST00000262593 36.09 44.70 38.64 0.94 0.66 0.82 1.84 1.97 2.01
ZNF385A ENST00000338010 36.09 28.59 30.58 0.94 1.16 0.80 1.83 1.29 1.47
AMHR2 ENST00000257863 36.10 50.02 41.28 0.94 0.66 0.75 1.82 2.01 2.02
MTBP ENST00000305949 36.10 53.51 43.16 0.94 0.65 0.65 1.82 1.70 1.99
XAB2 ENST00000358368 36.11 12.26 22.37 0.94 2.06 1.16 1.82 0.58 0.96
AGGF1 ENST00000312916 36.11 28.76 30.68 0.94 1.15 0.80 1.82 1.29 1.48
WNT7A ENST00000285018 36.12 37.98 35.25 0.94 0.77 0.86 1.82 1.71 1.76
ATXN7 ENST00000398590 36.12 11.05 21.73 0.94 2.09 1.25 1.82 0.52 0.93
SSTR1 ENST00000267377 36.13 28.31 30.43 0.94 1.16 0.80 1.81 1.22 1.46
IFT81 ENST00000242591 36.13 43.88 38.31 0.94 0.61 0.85 1.81 1.96 2.04
MEX3B ENST00000329713 36.14 29.00 30.83 0.94 1.15 0.78 1.81 1.31 1.49
DAG1 ENST00000545947 36.14 13.91 23.12 0.94 2.05 1.20 1.81 0.60 1.00
RGMA ENST00000557301 36.15 31.15 31.84 0.94 1.01 0.92 1.81 1.36 1.57
SNAP91 ENST00000439399 36.16 5.53 18.85 0.94 3.01 1.56 1.81 0.33 0.83

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