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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
CD97 ENST00000242786 78.00 31.23 54.12 0.33 1.00 0.59 0.67 1.38 1.75
C17orf70 ENST00000327787 78.00 41.41 60.14 0.33 0.62 0.47 0.67 1.80 1.61
VPREB3 ENST00000248948 78.01 93.18 88.73 0.33 0.28 0.20 0.67 0.30 0.28
SEPT12 ENST00000268231 78.01 92.35 88.34 0.33 0.25 0.22 0.67 0.30 0.30
EIF5AL1 ENST00000520547 78.02 90.52 87.43 0.34 0.25 0.28 0.67 0.37 0.31
OR4K1 ENST00000285600 78.02 96.46 90.29 0.34 0.22 0.15 0.67 0.19 0.21
LRP3 ENST00000253193 78.03 40.04 59.23 0.34 0.63 0.49 0.67 1.69 1.69
OTOL1 ENST00000327928 78.03 89.31 86.83 0.34 0.27 0.29 0.67 0.37 0.32
ZHX1-C8ORF76 ENST00000357082 78.04 76.29 80.49 0.34 0.43 0.39 0.67 0.86 0.51
RDH16 ENST00000398138 78.04 81.28 83.00 0.34 0.34 0.32 0.67 0.54 0.40
IZUMO4 ENST00000395301 78.05 88.14 86.32 0.34 0.24 0.33 0.67 0.38 0.33
HSPA6 ENST00000309758 78.05 74.70 79.65 0.34 0.54 0.38 0.67 0.96 0.53
GDPD4 ENST00000315938 78.06 63.15 73.42 0.34 0.47 0.42 0.67 1.31 0.76
KRT78 ENST00000304620 78.06 77.45 81.10 0.34 0.42 0.39 0.67 0.76 0.49
NEUROG1 ENST00000314744 78.07 93.09 88.66 0.34 0.28 0.20 0.67 0.30 0.28
CLMN ENST00000298912 78.07 38.20 58.21 0.34 0.77 0.48 0.67 1.70 1.64
KLF11 ENST00000305883 78.08 77.27 81.02 0.34 0.42 0.39 0.67 0.77 0.50
FAM47E-STBD1 ENST00000237642 78.08 91.46 87.90 0.34 0.23 0.24 0.67 0.32 0.32
SLURP1 ENST00000246515 78.09 69.22 76.76 0.34 0.56 0.34 0.67 1.13 0.61
ACCSL ENST00000378832 78.10 71.29 77.90 0.34 0.53 0.38 0.67 1.07 0.54
STAP2 ENST00000600324 78.10 77.49 81.14 0.34 0.42 0.39 0.67 0.78 0.49
ODF3L1 ENST00000332145 78.11 90.49 87.46 0.34 0.25 0.28 0.66 0.37 0.30
SH2B3 ENST00000341259 78.11 45.81 63.03 0.34 0.75 0.51 0.66 2.02 1.39
SIGLECL1 ENST00000316401 78.12 90.86 87.62 0.34 0.25 0.25 0.66 0.35 0.31
MYBBP1A ENST00000381556 78.12 65.93 74.97 0.34 0.54 0.40 0.66 1.24 0.66

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