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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
HIATL1 ENST00000375344 45.33 35.05 38.47 0.62 0.76 0.84 1.76 1.58 2.05
VPS37B ENST00000267202 45.33 34.72 38.33 0.62 0.78 0.85 1.75 1.54 2.04
ZNF331 ENST00000253144 45.34 11.52 26.55 0.62 2.11 0.99 1.75 0.57 1.25
TRPV6 ENST00000359396 45.34 36.09 39.06 0.61 0.81 0.78 1.75 1.59 2.06
NPFFR1 ENST00000277942 45.35 94.51 72.60 0.61 0.23 0.46 1.75 0.24 0.81
MTRF1 ENST00000379480 45.35 55.46 49.28 0.61 0.57 0.70 1.75 1.60 1.85
TJP2 ENST00000539225 45.36 33.05 37.44 0.59 0.85 0.86 1.75 1.49 2.01
NME7 ENST00000367811 45.36 50.05 46.38 0.59 0.66 0.67 1.75 1.99 1.90
IMMP1L ENST00000278200 45.37 76.39 61.60 0.59 0.43 0.46 1.76 0.86 1.48
BBS9 ENST00000242067 45.37 42.60 42.22 0.59 0.59 0.70 1.76 1.89 2.01
NEDD4 ENST00000338963 45.38 32.57 37.27 0.58 0.86 0.82 1.77 1.48 2.00
METTL17 ENST00000382985 45.39 59.81 51.74 0.58 0.52 0.62 1.76 1.37 1.93
CYP27B1 ENST00000228606 45.39 52.89 47.99 0.58 0.65 0.67 1.76 1.80 1.87
HOXD13 ENST00000392539 45.40 42.63 42.24 0.58 0.59 0.70 1.76 1.90 2.01
S100A6 ENST00000368720 45.40 85.31 67.10 0.58 0.25 0.51 1.76 0.45 1.16
ZNF296 ENST00000303809 45.41 14.97 28.37 0.58 1.92 0.80 1.76 0.64 1.29
TYROBP ENST00000262629 45.41 40.96 41.41 0.58 0.61 0.73 1.77 1.79 2.02
NOA1 ENST00000264230 45.42 39.67 40.70 0.58 0.68 0.81 1.76 1.66 2.04
PLXDC1 ENST00000315392 45.42 47.38 45.04 0.57 0.66 0.70 1.77 2.01 2.02
FAM212B ENST00000357260 45.43 58.77 51.15 0.57 0.54 0.65 1.77 1.43 1.90
USP16 ENST00000334352 45.43 40.24 41.04 0.57 0.61 0.76 1.76 1.73 2.04
TNFAIP8L3 ENST00000327536 45.44 89.00 69.35 0.57 0.27 0.43 1.76 0.35 0.98
TRIM55 ENST00000315962 45.44 64.39 54.49 0.57 0.48 0.57 1.76 1.22 1.75
MME ENST00000460393 45.45 46.89 44.77 0.57 0.71 0.65 1.75 1.94 2.05
MRPS9 ENST00000258455 45.45 52.99 48.09 0.57 0.66 0.66 1.76 1.78 1.89

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