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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
ZNF254 ENST00000357002 88.19 87.19 90.76 0.20 0.20 0.15 0.35 0.41 0.20
HES2 ENST00000377834 92.43 87.22 91.45 0.15 0.20 0.15 0.18 0.41 0.18
THEM6 ENST00000336138 94.05 87.22 93.36 0.10 0.20 0.11 0.13 0.41 0.15
PAEP ENST00000479141 95.98 87.18 94.36 0.11 0.20 0.10 0.11 0.41 0.12
SMR3B ENST00000304915 96.43 87.20 94.55 0.10 0.20 0.09 0.11 0.41 0.12
APOL1 ENST00000319136 99.22 87.21 95.95 0.11 0.20 0.07 0.12 0.41 0.10
IFNA14 ENST00000380222 95.84 98.13 98.92 0.11 0.20 0.10 0.11 0.16 0.04
LENG9 ENST00000333834 98.81 98.12 99.81 0.10 0.20 0.12 0.11 0.16 0.04
IFNW1 ENST00000380229 84.08 98.11 93.95 0.30 0.20 0.09 0.48 0.16 0.11
RP11-480I12.4 ENST00000330493 87.96 98.11 96.62 0.22 0.20 0.08 0.35 0.16 0.08
AC105020.1 ENST00000435356 90.75 98.10 96.93 0.16 0.20 0.08 0.23 0.16 0.07
C16orf3 ENST00000408886 95.66 98.10 98.95 0.11 0.20 0.10 0.11 0.16 0.04
C12orf61 ENST00000408887 88.08 98.09 95.89 0.20 0.20 0.07 0.35 0.16 0.11
KRTAP19-4 ENST00000334058 88.23 98.09 96.77 0.22 0.20 0.08 0.34 0.16 0.08
KRTAP19-2 ENST00000334055 87.28 98.08 95.52 0.23 0.20 0.08 0.38 0.16 0.11
C3orf56 ENST00000398112 98.74 98.08 99.68 0.10 0.20 0.12 0.11 0.16 0.04
AC112721.1 ENST00000409162 90.71 98.07 97.05 0.16 0.20 0.08 0.23 0.16 0.07
QRFP ENST00000343079 89.38 98.07 96.66 0.16 0.20 0.08 0.32 0.16 0.08
ZNF705D ENST00000400085 90.70 98.06 97.77 0.16 0.20 0.09 0.24 0.16 0.04
FAM27E2 ENST00000377529 90.68 98.06 97.31 0.16 0.20 0.08 0.24 0.16 0.07
KRTAP9-1 ENST00000398470 95.33 98.05 98.80 0.10 0.20 0.10 0.11 0.16 0.05
CTD-2144E22.5 ENST00000319817 90.65 98.05 98.13 0.16 0.20 0.09 0.24 0.16 0.05
AC145676.2 ENST00000514988 90.65 98.04 97.28 0.16 0.20 0.08 0.24 0.16 0.07
C6orf141 ENST00000529246 86.56 98.67 95.49 0.24 0.20 0.08 0.41 0.15 0.11
TAS2R50 ENST00000506868 99.45 98.04 99.82 0.11 0.20 0.12 0.12 0.16 0.04

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