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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
RSU1 ENST00000377921 16.02 45.38 28.84 1.53 0.68 0.81 0.79 1.99 1.31
SUGP1 ENST00000247001 16.02 10.75 11.03 1.53 2.11 2.19 0.79 0.51 0.44
TOMM40L ENST00000367988 16.03 25.18 18.57 1.53 1.32 1.59 0.79 1.02 0.81
POLE2 ENST00000216367 16.03 39.87 26.11 1.53 0.65 0.97 0.79 1.69 1.26
KCNJ10 ENST00000368089 16.04 44.37 28.40 1.53 0.62 0.78 0.79 1.96 1.29
MLLT10 ENST00000307729 16.04 4.71 7.74 1.53 3.27 2.67 0.80 0.31 0.33
NXT1 ENST00000254998 16.05 45.87 29.13 1.53 0.75 0.84 0.80 2.02 1.32
GFOD1 ENST00000379287 16.05 40.87 26.61 1.53 0.61 0.97 0.80 1.78 1.25
TBK1 ENST00000331710 16.06 18.96 15.27 1.53 1.52 1.83 0.80 0.75 0.66
SEMA3A ENST00000265362 16.06 12.63 11.96 1.53 2.09 2.28 0.80 0.58 0.46
MSANTD3 ENST00000395067 16.07 44.87 28.62 1.53 0.68 0.78 0.80 1.99 1.35
SLC4A2 ENST00000485713 16.07 12.74 12.00 1.52 2.09 2.29 0.80 0.59 0.47
C8orf44-SGK3 ENST00000519289 16.08 40.77 26.53 1.51 0.62 0.99 0.81 1.77 1.26
SGK3 ENST00000396596 16.08 40.81 26.58 1.51 0.62 0.97 0.81 1.78 1.25
CACNB3 ENST00000301050 16.09 36.81 24.50 1.51 0.75 1.08 0.81 1.66 1.08
DMTN ENST00000523266 16.09 17.64 14.59 1.51 1.58 1.97 0.81 0.73 0.59
PEG10 ENST00000482108 16.10 19.35 15.56 1.51 1.49 1.78 0.81 0.74 0.67
AQP3 ENST00000297991 16.10 38.36 25.32 1.51 0.75 1.05 0.81 1.72 1.16
NCL ENST00000322723 16.11 4.22 7.53 1.51 3.25 2.77 0.81 0.32 0.33
MAP1B ENST00000296755 16.11 2.32 6.60 1.51 3.63 3.00 0.81 0.29 0.32
ABCF2 ENST00000222388 16.12 23.13 17.52 1.51 1.46 1.63 0.80 0.90 0.75
RPS6 ENST00000380394 16.13 9.59 10.43 1.51 2.48 2.18 0.80 0.50 0.43
TULP4 ENST00000367097 16.13 2.20 6.51 1.51 3.66 3.04 0.80 0.29 0.32
PREX1 ENST00000371941 16.14 0.86 5.74 1.51 4.11 3.30 0.80 0.29 0.28
FIGN ENST00000333129 16.14 10.50 10.96 1.51 2.19 2.23 0.80 0.50 0.44

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