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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
C1QTNF1-AS1 ENST00000581579 92.46 68.30 83.90 0.15 0.52 0.35 0.18 1.20 0.43
C21orf67 ENST00000330551 92.46 84.32 91.46 0.15 0.28 0.15 0.18 0.44 0.18
CTB-58E17.5 ENST00000539023 92.47 99.00 98.32 0.15 0.15 0.09 0.18 0.15 0.05
OLIG1 ENST00000382348 92.47 47.88 71.98 0.15 0.59 0.42 0.18 1.97 0.81
AP001816.1 ENST00000527564 92.48 99.01 97.85 0.15 0.15 0.09 0.18 0.15 0.04
KRTAP22-2 ENST00000382830 92.48 99.01 98.32 0.15 0.15 0.09 0.18 0.15 0.05
C11orf89 ENST00000391480 92.49 99.02 98.04 0.15 0.15 0.09 0.18 0.15 0.05
C21orf119 ENST00000534991 92.50 99.02 98.33 0.15 0.15 0.09 0.18 0.15 0.05
TSTD1 ENST00000423014 92.50 53.59 75.23 0.15 0.62 0.37 0.18 1.71 0.67
RP11-520P18.5 ENST00000562505 92.51 86.04 92.20 0.15 0.25 0.14 0.18 0.43 0.16
C6ORF50 ENST00000356722 92.51 99.04 98.34 0.15 0.15 0.09 0.18 0.14 0.05
PRR9 ENST00000368744 92.52 95.53 95.31 0.15 0.23 0.08 0.18 0.21 0.10
RP11-817J15.3 ENST00000537079 92.52 95.15 95.93 0.15 0.23 0.07 0.18 0.21 0.10
EVA1B ENST00000270824 92.53 36.12 64.68 0.15 0.81 0.51 0.18 1.60 1.32
MTRNR2L13 ENST00000604093 92.53 99.06 98.35 0.15 0.15 0.10 0.18 0.14 0.05
SDIM1 ENST00000545867 92.54 99.07 98.36 0.15 0.15 0.10 0.18 0.14 0.05
RNF224 ENST00000445101 92.54 88.35 92.47 0.15 0.23 0.14 0.18 0.37 0.15
DLEU2L ENST00000371086 92.55 88.42 93.38 0.15 0.23 0.11 0.18 0.37 0.15
CXorf24 ENST00000357412 92.55 99.08 97.47 0.15 0.15 0.08 0.18 0.14 0.07
NME3 ENST00000219302 92.56 94.72 95.80 0.15 0.23 0.07 0.18 0.24 0.11
MBD3L5 ENST00000329753 92.56 92.64 95.54 0.15 0.29 0.08 0.18 0.31 0.11
AP006621.5 ENST00000530083 92.57 99.09 98.37 0.15 0.15 0.10 0.18 0.14 0.05
MAFG ENST00000357736 92.57 36.48 66.41 0.15 0.81 0.52 0.18 1.64 1.21
SHISA9 ENST00000424107 92.58 19.62 55.07 0.15 1.43 0.51 0.18 0.74 1.74
MAGEA9B ENST00000243314 92.58 99.09 98.37 0.15 0.15 0.10 0.18 0.14 0.05

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