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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
MRPS25 ENST00000253686 22.34 81.70 51.09 1.46 0.33 0.65 1.05 0.52 1.89
ZFP14 ENST00000270001 22.35 38.92 28.76 1.46 0.70 0.80 1.05 1.65 1.32
FXYD7 ENST00000270310 22.35 79.78 50.06 1.46 0.35 0.62 1.05 0.64 1.92
AMFR ENST00000290649 22.36 32.21 25.37 1.46 0.86 1.05 1.06 1.46 1.17
MOB1B ENST00000396051 22.36 48.65 33.68 1.46 0.63 0.90 1.06 1.99 1.73
EXOC5 ENST00000413566 22.37 4.98 11.35 1.46 3.25 2.20 1.06 0.32 0.45
TROVE2 ENST00000367446 22.37 21.16 19.81 1.46 1.46 1.49 1.06 0.81 0.85
PHF2 ENST00000359246 22.38 4.32 10.98 1.46 3.27 2.21 1.06 0.32 0.44
NKAIN2 ENST00000368417 22.39 41.85 30.31 1.46 0.61 0.84 1.06 1.80 1.44
SNAP23 ENST00000249647 22.39 16.71 17.43 1.46 1.70 1.62 1.06 0.71 0.75
CASP2 ENST00000310447 22.40 33.61 26.18 1.47 0.85 0.99 1.06 1.55 1.25
GPR34 ENST00000378142 22.40 36.82 27.78 1.47 0.76 0.90 1.06 1.66 1.27
COX5A ENST00000322347 22.41 41.28 30.02 1.47 0.61 0.81 1.06 1.82 1.46
ATP5C1 ENST00000356708 22.41 41.71 30.25 1.47 0.61 0.82 1.05 1.80 1.44
GPN1 ENST00000264718 22.42 40.84 29.81 1.47 0.61 0.85 1.05 1.78 1.43
PPP3CC ENST00000397775 22.42 22.90 20.80 1.47 1.47 1.47 1.05 0.90 0.88
RND1 ENST00000309739 22.43 25.25 21.95 1.47 1.29 1.18 1.05 1.03 0.97
PCIF1 ENST00000372409 22.43 3.20 10.39 1.47 3.46 2.19 1.05 0.28 0.43
MAEA ENST00000303400 22.44 21.52 20.02 1.47 1.42 1.49 1.04 0.81 0.85
MYL12A ENST00000217652 22.44 87.52 54.54 1.47 0.23 0.56 1.04 0.37 1.74
ZNF606 ENST00000341164 22.45 19.69 19.07 1.47 1.43 1.54 1.04 0.74 0.85
FLT1 ENST00000282397 22.45 8.31 12.97 1.48 2.52 2.09 1.04 0.45 0.53
CDH9 ENST00000231021 22.46 16.26 17.21 1.47 1.78 1.64 1.04 0.69 0.73
PPIL1 ENST00000373699 22.46 46.13 32.50 1.46 0.75 0.89 1.04 2.04 1.62
RAP1GAP2 ENST00000254695 22.47 14.14 16.12 1.46 2.06 1.71 1.04 0.59 0.66

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