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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
HSD17B7 ENST00000254521 51.34 64.75 58.08 0.59 0.48 0.47 1.84 1.24 1.65
NPPC ENST00000409852 51.34 81.70 68.51 0.59 0.33 0.47 1.84 0.52 1.06
C2ORF15 ENST00000302513 51.35 92.94 75.07 0.59 0.29 0.39 1.84 0.30 0.67
UQCC2 ENST00000607484 51.35 56.24 53.22 0.59 0.52 0.61 1.84 1.56 1.88
MTO1 ENST00000415954 51.36 33.50 40.61 0.59 0.84 0.81 1.84 1.53 2.05
NHLRC3 ENST00000379600 51.36 56.34 53.27 0.59 0.52 0.61 1.84 1.53 1.87
XRCC4 ENST00000511817 51.57 60.63 55.79 0.59 0.53 0.52 1.84 1.41 1.74
UBE2T ENST00000367274 51.68 70.72 61.94 0.58 0.48 0.48 1.84 1.09 1.45
CEP112 ENST00000392769 51.68 60.13 55.59 0.58 0.52 0.53 1.84 1.39 1.75
ALDH3A2 ENST00000339618 34.92 43.68 37.54 0.92 0.62 0.84 1.85 1.97 2.01
QRSL1 ENST00000369046 34.93 49.62 40.52 0.94 0.66 0.80 1.85 2.02 2.04
AC022532.1 ENST00000420338 34.93 80.32 57.59 0.94 0.37 0.51 1.85 0.58 1.67
SEMA3E ENST00000307792 34.94 34.94 33.08 0.94 0.76 0.87 1.85 1.55 1.66
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
ATL2 ENST00000378954 35.17 24.75 28.14 0.91 1.32 0.81 1.85 1.05 1.27
NFATC4 ENST00000413692 35.18 16.54 23.91 0.91 1.78 1.09 1.85 0.69 1.04
PEX6 ENST00000304611 36.06 31.41 31.95 0.94 0.96 0.91 1.85 1.42 1.58
BRDT ENST00000362005 49.63 34.57 40.36 0.54 0.80 0.80 1.85 1.54 2.02
TRABD ENST00000303434 49.64 37.25 41.67 0.54 0.76 0.72 1.85 1.66 2.01
SERTAD1 ENST00000357949 49.65 62.33 55.67 0.54 0.53 0.53 1.85 1.33 1.73
S100A4 ENST00000368716 49.65 91.63 73.45 0.54 0.23 0.40 1.85 0.32 0.76
HMGN2 ENST00000361427 49.66 22.31 34.23 0.54 1.52 0.86 1.85 0.82 1.76

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