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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
PAMR1 ENST00000278360 61.99 76.94 72.08 0.71 0.43 0.43 1.29 0.79 0.81
CDH17 ENST00000027335 61.99 52.79 57.29 0.71 0.65 0.51 1.29 1.80 1.68
OSBPL5 ENST00000263650 62.00 27.37 43.06 0.71 1.25 0.66 1.29 1.17 2.01
DSG2 ENST00000261590 62.00 41.32 50.74 0.71 0.62 0.66 1.29 1.82 1.84
TDRD10 ENST00000368480 62.01 51.16 56.39 0.71 0.66 0.51 1.28 1.90 1.73
SLC25A16 ENST00000609923 62.01 58.93 61.07 0.70 0.52 0.43 1.28 1.43 1.53
LAMC3 ENST00000361069 62.02 44.34 52.49 0.70 0.62 0.61 1.28 1.95 1.91
MRPL35 ENST00000337109 62.02 72.88 69.65 0.70 0.49 0.44 1.28 1.04 0.95
SGOL2 ENST00000357799 62.03 33.78 46.56 0.70 0.85 0.66 1.28 1.56 1.90
LACTB2 ENST00000276590 62.03 63.61 64.10 0.70 0.51 0.52 1.28 1.24 1.37
C2orf44 ENST00000295148 62.04 40.62 50.36 0.70 0.63 0.66 1.28 1.77 1.90
NAP1L3 ENST00000373079 62.04 49.51 55.42 0.70 0.65 0.49 1.29 2.03 1.72
COQ3 ENST00000254759 62.05 73.00 69.75 0.70 0.51 0.44 1.29 1.03 0.93
ZFP36L2 ENST00000282388 62.05 11.85 35.13 0.70 2.09 0.86 1.28 0.58 1.77
USP43 ENST00000285199 62.06 18.81 38.70 0.70 1.53 0.82 1.28 0.74 2.02
KLF8 ENST00000468660 62.06 72.17 69.21 0.70 0.52 0.44 1.28 1.04 0.98
SNAPC5 ENST00000316634 62.07 93.19 80.98 0.70 0.28 0.39 1.28 0.30 0.50
HBA2 ENST00000251595 62.07 95.90 82.38 0.70 0.22 0.33 1.28 0.20 0.44
LGALS9 ENST00000395473 62.08 54.03 58.12 0.70 0.65 0.48 1.28 1.69 1.65
RFXANK ENST00000303088 62.08 62.00 63.12 0.70 0.56 0.49 1.28 1.36 1.39
MRPS23 ENST00000313608 62.09 42.58 51.48 0.70 0.59 0.63 1.28 1.88 1.91
SIT1 ENST00000259608 62.09 65.83 65.50 0.70 0.54 0.52 1.28 1.22 1.29
TNKS1BP1 ENST00000532437 62.10 18.01 38.36 0.70 1.52 0.85 1.28 0.74 2.04
PXDC1 ENST00000380283 62.10 61.28 62.58 0.70 0.54 0.48 1.28 1.39 1.40
TTC29 ENST00000325106 62.11 53.56 57.85 0.70 0.63 0.51 1.27 1.70 1.66

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