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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
MMGT1 ENST00000305963 10.72 27.68 17.05 1.94 1.27 1.67 0.57 1.19 0.71
SLC39A14 ENST00000359741 10.73 27.64 17.04 1.94 1.27 1.67 0.57 1.18 0.70
PHB ENST00000300408 10.73 24.82 15.60 1.94 1.33 1.77 0.57 1.06 0.66
LBX1 ENST00000370193 10.74 30.41 18.56 1.94 1.09 1.61 0.57 1.39 0.81
FOXF1 ENST00000262426 10.74 12.66 9.11 1.94 2.10 2.37 0.57 0.58 0.38
RPL27A ENST00000314138 10.75 16.96 11.54 1.94 1.66 2.21 0.57 0.73 0.45
KSR2 ENST00000339824 10.75 2.33 3.89 1.92 3.64 3.74 0.57 0.29 0.23
RSPO3 ENST00000356698 10.76 30.95 18.86 1.92 1.05 1.56 0.57 1.35 0.83
PIN1 ENST00000247970 10.76 26.79 16.62 1.92 1.23 1.72 0.57 1.12 0.70
IRF1 ENST00000245414 10.77 9.69 7.59 1.91 2.45 2.75 0.57 0.50 0.33
UBE2J2 ENST00000400930 10.77 17.52 11.77 1.91 1.58 2.21 0.57 0.73 0.46
BDNF ENST00000438929 10.78 25.09 15.75 1.91 1.33 1.77 0.57 1.03 0.66
MYH7 ENST00000355349 10.78 29.53 18.11 1.92 1.10 1.67 0.57 1.39 0.78
RB1 ENST00000267163 10.79 0.59 3.12 1.92 4.14 3.93 0.57 0.28 0.24
POGZ ENST00000271715 10.79 1.82 3.69 1.94 3.78 3.82 0.57 0.26 0.23
SSBP1 ENST00000481508 10.80 48.24 27.67 1.94 0.63 0.95 0.57 2.00 1.27
ZBTB7B ENST00000417934 10.81 26.97 16.73 1.92 1.23 1.68 0.57 1.10 0.70
GIGYF2 ENST00000409451 10.81 0.27 2.96 1.94 4.10 3.99 0.57 0.29 0.23
PCF11 ENST00000298281 10.82 0.05 2.85 1.94 4.11 4.01 0.57 0.28 0.23
DNTTIP1 ENST00000372622 10.82 20.00 12.98 1.94 1.43 2.09 0.57 0.73 0.53
PFDN6 ENST00000395131 10.83 14.49 10.23 1.94 2.02 2.21 0.57 0.61 0.42
BAZ1A ENST00000360310 10.83 4.47 4.91 1.94 3.26 3.68 0.57 0.32 0.25
KHDRBS1 ENST00000327300 10.84 8.66 7.11 1.94 2.48 2.87 0.57 0.47 0.33
SPTLC2 ENST00000216484 10.84 18.19 12.08 1.94 1.49 2.29 0.57 0.75 0.48
WWP1 ENST00000517970 10.85 9.07 7.32 1.92 2.44 2.81 0.57 0.47 0.34

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