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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
SLC5A9 ENST00000236495 55.79 75.51 67.43 0.58 0.44 0.52 1.63 0.90 1.14
C6 ENST00000263413 55.79 52.84 53.73 0.58 0.65 0.62 1.63 1.80 1.80
LANCL1 ENST00000443314 55.80 69.44 63.90 0.58 0.54 0.51 1.63 1.13 1.38
ZNF345 ENST00000529555 55.80 77.91 68.91 0.58 0.42 0.46 1.62 0.79 1.04
PDZD9 ENST00000537222 55.81 71.15 64.92 0.58 0.51 0.51 1.63 1.06 1.33
MUSTN1 ENST00000446157 55.81 89.89 75.87 0.58 0.25 0.38 1.63 0.37 0.63
SLC5A11 ENST00000347898 55.82 59.60 57.70 0.58 0.52 0.49 1.63 1.41 1.67
PNLIP ENST00000369221 55.82 53.55 54.21 0.58 0.63 0.59 1.63 1.70 1.75
FRMD4B ENST00000398540 55.83 16.17 34.28 0.58 1.81 0.87 1.63 0.69 1.76
MOCS3 ENST00000244051 55.83 81.42 71.03 0.58 0.33 0.43 1.63 0.55 0.86
SLC10A4 ENST00000273861 55.84 50.06 52.18 0.57 0.66 0.61 1.63 1.99 1.90
HKDC1 ENST00000354624 55.84 49.09 51.62 0.57 0.66 0.62 1.63 2.04 1.92
NDUFB1 ENST00000329559 55.85 93.17 77.71 0.57 0.28 0.38 1.63 0.30 0.55
COMMD6 ENST00000355801 55.85 55.32 55.18 0.57 0.57 0.51 1.63 1.61 1.75
HSPBAP1 ENST00000306103 55.86 56.67 55.95 0.57 0.53 0.49 1.63 1.55 1.76
NT5DC2 ENST00000422318 55.86 37.83 45.57 0.57 0.80 0.68 1.63 1.70 1.97
AIM1 ENST00000369066 55.87 53.54 54.23 0.57 0.63 0.59 1.63 1.70 1.74
CCNB2 ENST00000288207 55.88 64.21 60.59 0.57 0.49 0.44 1.63 1.21 1.58
STK32A ENST00000397936 55.88 47.50 50.76 0.57 0.62 0.66 1.63 2.01 1.84
NELFA ENST00000382882 55.89 25.99 39.32 0.57 1.20 0.80 1.63 1.10 2.04
ZSCAN16 ENST00000340487 55.89 76.86 68.33 0.57 0.43 0.49 1.63 0.81 1.07
GSTM4 ENST00000369836 55.90 83.99 72.62 0.57 0.28 0.46 1.63 0.46 0.81
SAMD12 ENST00000314727 55.90 68.55 63.37 0.57 0.53 0.49 1.63 1.20 1.36
MND1 ENST00000240488 55.91 73.33 66.31 0.57 0.56 0.53 1.63 1.02 1.21
RAX ENST00000334889 55.91 48.08 51.07 0.57 0.63 0.66 1.63 1.99 1.89

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