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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
UNC45B ENST00000268876 48.30 49.84 47.92 0.56 0.66 0.66 1.82 2.02 1.89
UNC5CL ENST00000244565 48.30 72.05 60.76 0.56 0.52 0.44 1.81 1.03 1.61
ZFP69 ENST00000372706 48.31 60.78 54.04 0.56 0.56 0.59 1.81 1.39 1.76
ZNF653 ENST00000293771 48.31 33.03 39.01 0.56 0.85 0.78 1.81 1.49 2.06
NDUFS3 ENST00000263774 48.32 44.68 45.15 0.56 0.66 0.70 1.81 1.98 2.00
MAPK13 ENST00000211287 48.32 59.55 53.33 0.56 0.51 0.62 1.81 1.40 1.86
RBBP9 ENST00000337227 48.33 47.54 46.62 0.56 0.61 0.66 1.80 2.02 1.87
RPF1 ENST00000370654 48.33 66.05 57.10 0.56 0.56 0.52 1.80 1.21 1.71
UTP20 ENST00000261637 48.34 22.56 33.63 0.56 1.48 0.90 1.80 0.85 1.72
STXBP2 ENST00000221283 48.34 44.80 45.25 0.56 0.68 0.70 1.80 1.97 2.00
MYO5C ENST00000261839 48.35 44.00 44.80 0.56 0.61 0.66 1.80 1.97 2.04
NIPA2 ENST00000337451 48.35 17.34 31.07 0.56 1.59 0.84 1.80 0.75 1.52
TBX10 ENST00000335385 48.36 76.77 63.84 0.56 0.40 0.49 1.80 0.83 1.39
C21orf91 ENST00000284881 48.37 46.03 45.90 0.56 0.77 0.70 1.80 2.03 1.98
ADAMTSL1 ENST00000380548 48.37 27.00 35.78 0.56 1.23 0.85 1.80 1.12 1.78
MRPL49 ENST00000279242 48.38 77.86 64.37 0.56 0.42 0.51 1.80 0.79 1.34
LRRC20 ENST00000355790 48.38 65.43 56.72 0.56 0.53 0.52 1.80 1.25 1.71
TARSL2 ENST00000335968 48.39 47.92 46.88 0.56 0.59 0.68 1.80 1.99 1.88
IER3IP1 ENST00000256433 48.39 74.26 62.10 0.56 0.53 0.48 1.81 1.01 1.44
ANKRD55 ENST00000341048 48.40 44.08 44.89 0.56 0.59 0.68 1.80 1.98 2.04
HSD11B2 ENST00000326152 48.40 48.42 47.15 0.56 0.63 0.67 1.81 2.02 1.89
RTN4IP1 ENST00000369063 48.41 52.61 49.40 0.56 0.68 0.70 1.82 1.81 1.83
UACA ENST00000322954 48.41 51.37 48.79 0.56 0.63 0.70 1.82 1.89 1.86
PBK ENST00000301905 48.42 63.16 55.46 0.56 0.47 0.51 1.82 1.31 1.74
MRPL40 ENST00000333130 48.42 41.54 43.36 0.56 0.62 0.63 1.82 1.82 2.00

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