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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
SDPR ENST00000304141 65.73 89.75 81.10 0.58 0.27 0.39 1.07 0.37 0.49
FAM83A ENST00000518448 65.74 76.78 74.08 0.58 0.40 0.38 1.07 0.83 0.69
RFWD3 ENST00000361070 65.74 41.04 52.72 0.58 0.59 0.61 1.07 1.81 1.88
ZMYM5 ENST00000382905 65.75 62.20 65.49 0.58 0.52 0.52 1.06 1.34 1.29
MRPS24 ENST00000317534 65.75 61.85 65.28 0.58 0.57 0.53 1.06 1.36 1.31
OR52R1 ENST00000356069 65.76 95.36 83.89 0.58 0.24 0.35 1.06 0.21 0.43
WEE2 ENST00000397541 65.76 42.13 53.34 0.58 0.61 0.62 1.06 1.86 1.85
AQP8 ENST00000219660 65.77 61.04 64.79 0.58 0.54 0.51 1.06 1.39 1.32
PCDHB2 ENST00000194155 65.77 62.35 65.65 0.58 0.53 0.51 1.06 1.33 1.29
DNAJC21 ENST00000382021 65.78 38.71 51.36 0.59 0.70 0.63 1.06 1.67 1.90
SLC7A2 ENST00000004531 65.78 55.78 61.46 0.59 0.52 0.44 1.06 1.58 1.47
DMPK ENST00000343373 65.79 26.53 44.75 0.59 1.19 0.63 1.06 1.12 2.06
OR52N4 ENST00000317254 65.79 94.94 83.77 0.59 0.23 0.34 1.06 0.23 0.41
TCOF1 ENST00000504761 65.80 12.00 37.14 0.59 2.07 0.81 1.06 0.57 1.97
LRRC52 ENST00000294818 65.80 84.21 78.27 0.59 0.27 0.38 1.06 0.44 0.55
SLC9A3R2 ENST00000424542 65.81 36.10 49.94 0.59 0.81 0.61 1.06 1.59 1.89
RGN ENST00000397180 65.81 54.36 60.64 0.61 0.61 0.44 1.05 1.68 1.60
KEL ENST00000355265 65.82 59.11 63.68 0.61 0.49 0.49 1.05 1.43 1.39
RPA3 ENST00000223129 65.82 96.66 84.59 0.61 0.23 0.34 1.05 0.20 0.40
C19orf12 ENST00000392278 65.83 58.58 63.34 0.61 0.54 0.48 1.05 1.42 1.36
DRC1 ENST00000288710 65.83 58.45 63.24 0.61 0.54 0.49 1.06 1.39 1.36
IGHMBP2 ENST00000255078 65.84 52.53 59.45 0.61 0.66 0.49 1.06 1.83 1.70
ACAD10 ENST00000455480 65.84 60.78 64.66 0.61 0.56 0.51 1.06 1.39 1.32
ETV3L ENST00000454449 65.85 76.73 74.13 0.61 0.40 0.39 1.07 0.83 0.69
SFT2D2 ENST00000271375 65.85 47.17 56.26 0.61 0.66 0.49 1.07 2.00 1.76

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