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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
ZBP1 ENST00000371173 97.38 82.01 92.38 0.10 0.35 0.14 0.11 0.50 0.15
SSX7 ENST00000298181 96.21 89.65 95.70 0.12 0.27 0.07 0.11 0.36 0.11
ANKRD18A ENST00000399703 96.80 42.35 72.23 0.11 0.61 0.43 0.11 1.90 0.82
FRG2 ENST00000378763 97.97 89.01 96.23 0.11 0.27 0.07 0.11 0.35 0.09
VN1R2 ENST00000341702 96.21 99.37 99.41 0.12 0.16 0.11 0.11 0.12 0.05
LILRA4 ENST00000291759 97.39 77.06 90.26 0.10 0.42 0.16 0.11 0.78 0.22
SPATA31D1 ENST00000344803 98.56 77.90 91.19 0.10 0.42 0.15 0.11 0.79 0.18
DEFB129 ENST00000246105 96.80 92.77 97.38 0.09 0.29 0.08 0.11 0.30 0.07
KLRC2 ENST00000381902 97.98 89.73 96.63 0.11 0.27 0.08 0.11 0.37 0.08
CNBD1 ENST00000518476 96.22 85.95 93.85 0.12 0.28 0.10 0.11 0.43 0.12
PIWIL3 ENST00000332271 97.39 67.01 85.56 0.10 0.53 0.33 0.11 1.24 0.35
C6orf195 ENST00000296847 98.56 99.71 99.92 0.10 0.17 0.12 0.11 0.11 0.04
OR7E24 ENST00000456448 96.81 99.52 99.11 0.09 0.16 0.11 0.11 0.13 0.04
ZNF90 ENST00000418063 96.22 86.18 94.00 0.12 0.27 0.09 0.11 0.42 0.11
RP11-3B7.1 ENST00000440528 97.98 97.75 99.45 0.11 0.21 0.11 0.11 0.17 0.05
ZNF17 ENST00000601808 97.40 78.53 90.97 0.10 0.40 0.15 0.11 0.74 0.20
AC140481.2 ENST00000409982 96.81 85.40 93.86 0.09 0.25 0.09 0.11 0.44 0.12
LCN10 ENST00000497771 98.57 73.56 89.16 0.10 0.52 0.19 0.11 1.03 0.25
ZNF853 ENST00000457543 96.23 23.45 60.32 0.12 1.42 0.47 0.11 0.93 1.59
C21orf128 ENST00000329015 97.99 96.58 99.12 0.11 0.23 0.11 0.11 0.19 0.04
NBPF10 ENST00000342960 97.40 97.32 99.16 0.10 0.23 0.11 0.11 0.19 0.04
XAGE5 ENST00000351072 96.82 91.83 97.07 0.09 0.23 0.08 0.11 0.32 0.07
S100A7A ENST00000368729 96.23 96.30 98.49 0.12 0.22 0.10 0.11 0.19 0.05
DDTL ENST00000215770 98.57 91.57 97.66 0.10 0.23 0.09 0.11 0.33 0.06
GSDMC ENST00000276708 97.99 67.94 86.19 0.11 0.52 0.33 0.11 1.17 0.33

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