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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
POP5 ENST00000357500 40.94 83.90 63.62 0.84 0.28 0.49 1.72 0.46 1.39
GPX8 ENST00000503787 40.94 47.32 42.36 0.84 0.67 0.68 1.72 2.01 2.02
FGFR3 ENST00000340107 40.95 30.91 34.10 0.84 1.06 0.91 1.72 1.36 1.75
CLDN3 ENST00000395145 40.95 39.88 38.68 0.84 0.63 0.82 1.72 1.69 2.02
CNTNAP2 ENST00000361727 40.96 27.72 32.53 0.84 1.27 0.89 1.72 1.18 1.61
MPP2 ENST00000269095 40.96 45.56 41.48 0.84 0.73 0.73 1.72 1.99 2.02
IARS2 ENST00000302637 40.97 16.14 26.72 0.84 1.82 1.00 1.72 0.69 1.27
CCL21 ENST00000259607 40.97 68.74 54.39 0.84 0.53 0.58 1.72 1.17 1.75
SPRED2 ENST00000356388 40.98 55.69 47.06 0.84 0.52 0.68 1.71 1.60 1.88
KIF18A ENST00000263181 40.98 23.73 30.60 0.84 1.39 0.80 1.72 0.93 1.47
NAP1L4 ENST00000380542 40.99 19.82 28.56 0.84 1.42 0.80 1.72 0.74 1.34
DCLRE1A ENST00000361384 40.99 39.63 38.59 0.84 0.68 0.84 1.71 1.65 2.01
EP400 ENST00000389561 41.00 6.32 21.79 0.85 2.69 1.24 1.71 0.36 0.94
MINOS1-NBL1 ENST00000602662 41.01 73.00 56.84 0.85 0.51 0.52 1.71 1.03 1.70
UTP3 ENST00000254803 41.01 55.55 47.01 0.85 0.56 0.70 1.71 1.60 1.87
ZMYND15 ENST00000573751 41.02 51.25 44.71 0.85 0.65 0.62 1.71 1.90 2.06
ZNF354A ENST00000335815 41.02 41.96 39.84 0.85 0.61 0.77 1.71 1.83 2.03
CTBS ENST00000370630 41.03 65.06 52.30 0.85 0.51 0.59 1.72 1.24 1.92
PTPRE ENST00000254667 41.03 23.51 30.53 0.85 1.40 0.80 1.72 0.92 1.47
TMF1 ENST00000398559 41.04 25.89 31.67 0.85 1.21 0.89 1.72 1.08 1.59
WIPF1 ENST00000392547 41.04 18.04 27.68 0.85 1.53 0.94 1.72 0.74 1.27
SRL ENST00000399609 41.05 68.90 54.53 0.85 0.54 0.56 1.72 1.16 1.75
RINT1 ENST00000257700 41.05 41.65 39.71 0.85 0.62 0.78 1.72 1.80 2.03
SCARF1 ENST00000263071 41.06 38.22 37.89 0.85 0.77 0.85 1.72 1.70 2.01
ABHD8 ENST00000247706 41.06 12.91 25.06 0.85 2.07 1.05 1.72 0.59 1.15

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