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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
CHD9 ENST00000566029 10.21 3.57 4.17 2.02 3.38 3.78 0.54 0.30 0.23
VPS29 ENST00000360579 10.21 27.87 16.85 2.02 1.21 1.70 0.54 1.19 0.70
DGKI ENST00000288490 10.22 12.74 8.85 2.02 2.09 2.48 0.54 0.59 0.38
KLC1 ENST00000452929 10.22 17.80 11.65 2.04 1.52 2.21 0.54 0.72 0.47
PSMD11 ENST00000261712 10.23 3.46 4.14 2.04 3.40 3.78 0.54 0.29 0.23
OTX1 ENST00000282549 10.23 21.01 13.22 2.04 1.43 2.09 0.54 0.83 0.53
ABI2 ENST00000261017 10.24 22.41 14.01 2.04 1.51 2.05 0.54 0.82 0.60
SENP2 ENST00000296257 10.24 12.53 8.73 2.02 2.10 2.49 0.54 0.58 0.37
CMPK1 ENST00000371873 10.25 21.80 13.69 2.02 1.46 2.04 0.54 0.81 0.58
ATP6V1G2 ENST00000303892 10.25 67.48 37.10 2.02 0.54 0.80 0.54 1.20 1.95
RAB33A ENST00000257017 10.26 34.12 20.27 2.02 0.84 1.48 0.54 1.54 0.89
MAP3K5 ENST00000359015 10.26 14.89 10.16 2.02 1.94 2.25 0.54 0.62 0.42
YPEL4 ENST00000524669 10.27 51.38 28.98 2.02 0.63 0.81 0.54 1.89 1.31
RER1 ENST00000605895 10.27 28.45 17.20 2.02 1.15 1.64 0.54 1.24 0.73
EFNB2 ENST00000245323 10.28 6.77 5.80 2.02 2.66 3.33 0.54 0.37 0.28
TFAP2B ENST00000393655 10.28 9.42 7.20 2.02 2.47 2.83 0.54 0.49 0.34
FZD2 ENST00000315323 10.29 22.70 14.21 2.02 1.46 1.99 0.54 0.88 0.59
PITPNC1 ENST00000581322 10.29 9.06 7.01 2.04 2.43 2.88 0.54 0.47 0.33
ADSS ENST00000366535 10.30 21.79 13.70 2.04 1.46 2.05 0.54 0.81 0.58
TMEM65 ENST00000297632 10.30 44.55 25.52 2.04 0.65 1.05 0.54 1.97 1.19
RASGRP1 ENST00000310803 10.31 11.67 8.35 2.04 2.10 2.53 0.54 0.57 0.37
CCDC88A ENST00000336838 10.31 2.24 3.66 2.04 3.66 3.83 0.54 0.30 0.23
PTPN2 ENST00000309660 10.32 5.70 5.34 2.04 2.94 3.54 0.54 0.34 0.25
GPR173 ENST00000332582 10.32 21.16 13.37 2.04 1.46 2.05 0.54 0.81 0.55
TPR ENST00000367478 10.33 1.46 3.34 2.04 3.92 3.90 0.54 0.26 0.23

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