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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
ALPI ENST00000295463 82.00 78.39 83.56 0.30 0.43 0.33 0.57 0.74 0.40
HSD11B1L ENST00000423665 82.01 54.83 70.76 0.30 0.57 0.43 0.57 1.63 0.86
CAPN13 ENST00000295055 82.01 60.92 74.35 0.30 0.56 0.40 0.57 1.41 0.70
OR52M1 ENST00000360213 82.02 97.02 92.20 0.30 0.24 0.14 0.57 0.19 0.16
NDUFB7 ENST00000215565 82.02 86.03 87.20 0.30 0.25 0.28 0.57 0.43 0.31
LENG1 ENST00000222224 82.03 90.86 89.58 0.30 0.25 0.18 0.57 0.35 0.23
CR1 ENST00000367049 82.03 51.63 68.86 0.30 0.62 0.46 0.57 1.88 1.04
SLC38A8 ENST00000299709 82.04 94.56 91.21 0.30 0.23 0.15 0.57 0.24 0.18
MC1R ENST00000555147 82.04 97.25 92.32 0.30 0.23 0.14 0.57 0.19 0.15
EFHC2 ENST00000420999 82.05 3.20 40.79 0.30 3.46 0.81 0.57 0.28 2.04
ZNF524 ENST00000591046 82.05 75.79 82.28 0.30 0.43 0.34 0.57 0.88 0.45
ADAMDEC1 ENST00000256412 82.06 70.44 79.52 0.30 0.52 0.38 0.56 1.08 0.52
FADD ENST00000301838 82.06 70.01 79.32 0.30 0.53 0.39 0.56 1.13 0.53
NDUFS6 ENST00000274137 82.07 72.71 80.71 0.30 0.48 0.39 0.56 1.03 0.52
ZBED1 ENST00000381223 82.07 40.91 62.33 0.30 0.61 0.48 0.56 1.78 1.41
RAB41 ENST00000276066 82.08 78.44 83.65 0.30 0.43 0.34 0.56 0.73 0.40
GAPT ENST00000396776 82.08 92.50 90.34 0.30 0.28 0.15 0.56 0.30 0.21
KRTAP10-1 ENST00000400375 82.09 84.10 86.32 0.30 0.27 0.33 0.56 0.45 0.33
SPRR2F ENST00000468739 82.09 94.04 91.01 0.30 0.25 0.15 0.57 0.26 0.20
FAM109A ENST00000361483 82.10 89.08 88.71 0.30 0.27 0.20 0.57 0.35 0.28
TOP1MT ENST00000329245 82.10 84.21 86.36 0.30 0.27 0.33 0.57 0.44 0.33
CYP3A43 ENST00000222382 82.11 60.89 74.37 0.30 0.56 0.40 0.57 1.41 0.70
OR4F17 ENST00000585993 82.11 88.44 88.40 0.30 0.23 0.22 0.57 0.37 0.30
MT1E ENST00000306061 82.12 90.07 89.19 0.30 0.25 0.19 0.57 0.37 0.25
RBM12B-AS1 ENST00000391680 82.12 94.66 91.30 0.30 0.23 0.15 0.57 0.24 0.18

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