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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
ATP4A ENST00000262623 27.25 38.44 31.07 1.23 0.75 0.84 1.41 1.70 1.52
ZC3H12C ENST00000278590 27.26 7.12 14.98 1.21 2.58 1.87 1.41 0.37 0.63
PARP1 ENST00000366794 27.26 23.05 23.24 1.21 1.44 1.19 1.41 0.91 1.01
APBB2 ENST00000508593 27.27 22.21 22.90 1.21 1.53 1.19 1.41 0.81 0.97
UBXN1 ENST00000294119 27.27 21.76 22.66 1.21 1.46 1.18 1.40 0.81 0.97
BOLA3 ENST00000327428 27.28 58.43 41.05 1.21 0.54 0.75 1.41 1.38 2.05
SH3BGRL3 ENST00000270792 27.28 57.48 40.57 1.21 0.56 0.81 1.40 1.48 2.04
ELFN1 ENST00000424383 27.29 3.33 12.87 1.21 3.42 2.11 1.40 0.27 0.53
EDN1 ENST00000379375 27.29 33.12 28.39 1.21 0.82 0.78 1.40 1.51 1.29
SYT4 ENST00000255224 27.30 27.46 25.47 1.21 1.25 1.02 1.40 1.17 1.18
SLC30A4 ENST00000261867 27.30 29.19 26.35 1.21 1.13 1.00 1.41 1.35 1.26
CACHD1 ENST00000290039 27.31 28.83 26.23 1.21 1.15 1.00 1.41 1.29 1.26
FAM172A ENST00000395965 27.31 37.94 30.87 1.21 0.78 0.77 1.41 1.70 1.49
TRHR ENST00000518632 27.32 32.31 27.99 1.21 0.86 0.82 1.41 1.46 1.27
NDUFA1 ENST00000371437 27.32 65.68 45.17 1.21 0.53 0.70 1.41 1.22 2.00
DAD1 ENST00000250498 27.33 73.70 49.41 1.23 0.52 0.70 1.41 1.02 1.83
TMX3 ENST00000299608 27.33 30.75 27.19 1.21 1.06 0.99 1.41 1.36 1.25
ZNF202 ENST00000336139 27.34 19.26 21.39 1.21 1.47 1.33 1.41 0.76 0.91
LRP8 ENST00000306052 27.34 6.03 14.44 1.21 2.83 2.00 1.41 0.35 0.58
RFFL ENST00000315249 27.35 26.99 25.29 1.21 1.23 1.05 1.41 1.12 1.15
LDHA ENST00000540430 27.35 33.98 28.80 1.21 0.84 0.80 1.41 1.55 1.32
MPRIP ENST00000395811 27.36 12.39 17.77 1.21 2.06 1.66 1.41 0.59 0.78
PTPN5 ENST00000358540 27.36 29.62 26.63 1.21 1.10 0.99 1.41 1.39 1.25
FMNL1 ENST00000331495 27.37 8.05 15.53 1.21 2.53 1.80 1.41 0.44 0.67
ZNF248 ENST00000395867 27.37 23.55 23.55 1.21 1.39 1.19 1.41 0.93 1.01

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