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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
RASA4B ENST00000541662 7.62 69.41 36.66 2.73 0.56 0.84 0.40 1.14 1.93
KHSRP ENST00000398148 7.63 0.57 1.93 2.73 4.16 4.15 0.40 0.28 0.24
NPTN ENST00000345330 7.63 8.87 5.56 2.73 2.44 3.40 0.40 0.48 0.26
CTNNA2 ENST00000466387 7.64 18.25 10.50 2.73 1.49 2.18 0.40 0.74 0.43
HIC2 ENST00000443632 7.64 4.51 3.51 2.73 3.26 3.84 0.40 0.32 0.23
HDLBP ENST00000391975 7.65 3.22 2.86 2.73 3.46 4.01 0.40 0.28 0.23
SPI1 ENST00000227163 7.65 8.53 5.39 2.73 2.52 3.49 0.40 0.46 0.25
VCL ENST00000211998 7.66 17.86 10.32 2.72 1.51 2.19 0.40 0.72 0.43
CHUK ENST00000370397 7.66 10.84 6.63 2.72 2.14 3.00 0.40 0.50 0.32
KIAA1109 ENST00000264501 7.67 18.46 10.69 2.72 1.48 2.18 0.40 0.76 0.43
ATP6V0A1 ENST00000264649 7.68 10.32 6.31 2.72 2.25 3.11 0.40 0.50 0.32
SUV39H1 ENST00000376687 7.68 7.79 4.99 2.73 2.56 3.69 0.40 0.43 0.25
TNPO3 ENST00000265388 7.69 26.25 14.75 2.73 1.19 1.96 0.40 1.08 0.62
RPS24 ENST00000440692 7.69 29.97 16.67 2.73 1.09 1.70 0.40 1.42 0.70
HECA ENST00000367658 7.70 23.09 12.96 2.73 1.46 2.09 0.40 0.91 0.53
ASH2L ENST00000343823 7.70 6.40 4.31 2.73 2.63 3.75 0.40 0.37 0.24
IMPDH2 ENST00000326739 7.71 41.02 22.57 2.73 0.59 1.16 0.40 1.81 0.96
CHD7 ENST00000423902 7.71 0.35 1.87 2.73 4.14 4.18 0.40 0.28 0.24
WDR47 ENST00000400794 7.72 18.16 10.51 2.73 1.51 2.18 0.40 0.74 0.43
TOB1 ENST00000499247 7.72 12.77 7.60 2.73 2.09 2.73 0.40 0.59 0.33
NFYB ENST00000240055 7.73 60.70 32.43 2.73 0.54 0.91 0.40 1.40 1.61
GOLGA7 ENST00000357743 7.73 33.52 18.59 2.73 0.85 1.58 0.40 1.53 0.81
LMTK3 ENST00000270238 7.74 4.84 3.68 2.73 3.28 3.82 0.40 0.31 0.23
ASNA1 ENST00000591090 7.74 17.91 10.39 2.72 1.54 2.19 0.40 0.73 0.43
ZBTB44 ENST00000525842 7.75 2.67 2.70 2.72 3.53 4.01 0.40 0.29 0.23

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