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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
KIF26A ENST00000423312 85.23 18.03 50.67 0.28 1.52 0.66 0.47 0.74 1.85
GTF2IRD2 ENST00000405086 85.23 67.55 79.68 0.28 0.53 0.38 0.47 1.20 0.53
AADACL2 ENST00000356517 85.24 84.81 88.19 0.28 0.27 0.23 0.47 0.42 0.30
SPATA2L ENST00000289805 85.24 45.69 67.28 0.28 0.75 0.52 0.47 2.01 1.15
SLAMF7 ENST00000368043 85.25 39.57 63.61 0.28 0.68 0.49 0.47 1.65 1.39
HIST1H4F ENST00000377745 85.25 90.59 90.95 0.28 0.25 0.15 0.47 0.37 0.20
OVCH1 ENST00000318184 85.26 68.23 80.08 0.28 0.52 0.35 0.47 1.21 0.52
OR8H2 ENST00000313503 85.26 93.77 92.19 0.28 0.27 0.14 0.47 0.26 0.16
FCER2 ENST00000346664 85.27 70.96 81.47 0.28 0.49 0.35 0.47 1.05 0.48
DPPA2 ENST00000478945 85.27 76.48 84.14 0.28 0.42 0.34 0.47 0.84 0.42
KRBA1 ENST00000255992 85.28 58.52 74.80 0.28 0.54 0.39 0.47 1.39 0.66
FAM86C1 ENST00000359244 85.28 96.45 93.64 0.28 0.22 0.13 0.47 0.19 0.15
NLRP12 ENST00000324134 85.29 74.05 83.03 0.28 0.53 0.30 0.47 1.03 0.40
GPIHBP1 ENST00000330824 85.30 57.67 74.36 0.28 0.56 0.40 0.47 1.48 0.70
SYCN ENST00000318438 85.30 92.39 91.66 0.28 0.25 0.14 0.47 0.30 0.18
TCN1 ENST00000257264 85.31 84.25 87.91 0.28 0.28 0.24 0.47 0.44 0.32
WDR90 ENST00000293879 85.31 69.88 80.95 0.28 0.54 0.39 0.47 1.15 0.50
CCDC105 ENST00000292574 85.32 64.26 77.95 0.28 0.49 0.38 0.47 1.20 0.54
C12orf52 ENST00000548278 85.32 84.76 88.20 0.28 0.27 0.23 0.47 0.42 0.30
C19orf26 ENST00000590083 85.33 24.04 54.20 0.28 1.37 0.59 0.47 0.96 1.74
FAM203A ENST00000347708 85.33 91.27 91.23 0.28 0.23 0.15 0.47 0.34 0.18
KRTAP12-3 ENST00000397907 85.34 99.91 95.24 0.28 0.17 0.08 0.47 0.10 0.10
OR5H1 ENST00000354565 85.34 92.29 91.64 0.28 0.25 0.14 0.47 0.30 0.18
GCSAM ENST00000484193 85.35 57.54 74.31 0.28 0.57 0.40 0.47 1.47 0.70
KRTAP5-10 ENST00000398531 85.35 97.37 94.11 0.28 0.22 0.09 0.47 0.19 0.12

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