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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
SFR1 ENST00000369727 65.34 89.66 80.80 0.56 0.27 0.39 1.12 0.36 0.52
INCENP ENST00000394818 65.35 14.86 38.39 0.56 1.92 0.84 1.12 0.62 2.04
BDP1 ENST00000358731 65.35 30.25 46.46 0.56 1.09 0.67 1.12 1.40 1.92
UPB1 ENST00000326010 65.36 70.63 70.22 0.56 0.51 0.43 1.12 1.09 0.91
GPR110 ENST00000371253 65.36 68.39 68.92 0.56 0.52 0.46 1.12 1.20 1.04
SMIM7 ENST00000487416 65.37 78.96 75.10 0.56 0.40 0.39 1.12 0.69 0.67
NAP1L2 ENST00000373517 65.37 26.32 44.31 0.56 1.19 0.61 1.12 1.08 2.04
CASC1 ENST00000395987 65.38 54.66 60.55 0.56 0.58 0.44 1.12 1.65 1.58
MKNK2 ENST00000250896 65.38 38.46 50.99 0.56 0.75 0.66 1.12 1.70 1.86
CCDC97 ENST00000269967 65.39 79.86 75.59 0.56 0.35 0.38 1.12 0.61 0.64
HSDL1 ENST00000219439 65.39 53.84 60.05 0.56 0.63 0.48 1.12 1.70 1.61
IRGQ ENST00000422989 65.40 39.57 51.65 0.56 0.68 0.62 1.12 1.65 1.92
TMED3 ENST00000299705 65.40 53.97 60.08 0.56 0.65 0.48 1.12 1.70 1.61
SH2D6 ENST00000340326 65.41 81.67 76.62 0.56 0.33 0.37 1.12 0.52 0.61
LECT2 ENST00000274507 65.42 76.28 73.62 0.56 0.43 0.40 1.12 0.86 0.74
SHQ1 ENST00000325599 65.42 66.35 67.75 0.56 0.54 0.52 1.12 1.20 1.12
CAPN10 ENST00000391984 65.43 55.41 61.04 0.56 0.58 0.43 1.12 1.60 1.55
MOGAT2 ENST00000198801 65.43 41.13 52.58 0.56 0.59 0.61 1.12 1.82 1.89
QPCT ENST00000338415 65.44 80.98 76.31 0.56 0.35 0.35 1.12 0.56 0.61
RD3 ENST00000367002 65.44 88.27 80.19 0.56 0.23 0.35 1.12 0.37 0.52
TEX9 ENST00000352903 65.45 81.88 76.76 0.56 0.35 0.34 1.11 0.51 0.61
PLA2G12A ENST00000243501 65.45 76.25 73.64 0.56 0.43 0.40 1.11 0.86 0.74
SNX31 ENST00000311812 65.46 58.01 62.65 0.56 0.54 0.51 1.11 1.44 1.40
CENPK ENST00000396679 65.46 76.38 73.71 0.56 0.43 0.42 1.11 0.86 0.71
OR10A4 ENST00000379829 65.47 88.40 80.26 0.56 0.23 0.37 1.11 0.37 0.51

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