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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
PSTK ENST00000368887 68.18 54.25 61.93 0.56 0.62 0.48 1.02 1.70 1.45
SRXN1 ENST00000381962 68.19 81.02 77.79 0.56 0.35 0.38 1.02 0.55 0.54
MRPL30 ENST00000338148 68.19 63.20 67.51 0.56 0.47 0.51 1.02 1.31 1.14
C2orf15 ENST00000512183 68.20 63.23 67.53 0.56 0.47 0.51 1.01 1.31 1.13
ACOX2 ENST00000302819 68.20 48.90 58.63 0.56 0.63 0.52 1.01 2.04 1.65
SYDE1 ENST00000342784 68.21 19.50 42.08 0.56 1.46 0.71 1.01 0.74 1.99
SRRM2 ENST00000301740 68.21 2.03 33.27 0.56 3.73 0.87 1.01 0.29 1.70
ZNF101 ENST00000592502 68.22 35.59 50.98 0.56 0.77 0.66 1.01 1.58 1.85
TTC4 ENST00000371281 68.22 48.68 58.53 0.56 0.63 0.51 1.01 1.99 1.64
TLR1 ENST00000308979 68.23 90.12 82.57 0.56 0.25 0.32 1.01 0.38 0.43
RNF148 ENST00000434824 68.24 79.84 77.20 0.56 0.35 0.35 1.01 0.61 0.59
CNTN6 ENST00000446702 68.24 64.40 68.31 0.56 0.48 0.49 1.01 1.22 1.07
FCRLB ENST00000367948 68.25 80.82 77.74 0.56 0.35 0.38 1.01 0.57 0.55
C3orf62 ENST00000343010 68.25 75.49 74.77 0.56 0.44 0.40 1.00 0.90 0.66
RBM19 ENST00000545145 68.26 38.23 52.55 0.56 0.76 0.61 1.00 1.70 1.90
SLC47A1 ENST00000270570 68.26 64.57 68.39 0.56 0.48 0.47 1.00 1.22 1.05
RPH3AL ENST00000331302 68.27 72.65 73.20 0.56 0.47 0.43 1.00 1.04 0.79
WFS1 ENST00000226760 68.27 95.39 85.19 0.56 0.24 0.34 1.00 0.21 0.37
C11orf53 ENST00000280325 68.28 74.00 73.93 0.56 0.54 0.40 0.99 1.02 0.70
CUZD1 ENST00000368904 68.28 63.92 68.06 0.56 0.48 0.51 0.99 1.22 1.10
KRI1 ENST00000312962 68.29 47.00 57.62 0.56 0.70 0.51 0.99 1.97 1.68
ZFYVE21 ENST00000216602 68.29 31.42 48.72 0.56 0.96 0.68 1.00 1.42 1.85
GRWD1 ENST00000253237 68.30 37.15 51.88 0.56 0.78 0.62 1.00 1.66 1.94
MSRB2 ENST00000376510 68.30 82.08 78.44 0.56 0.34 0.38 1.00 0.51 0.54
DZANK1 ENST00000262547 68.31 63.94 68.09 0.56 0.48 0.51 1.00 1.21 1.10

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