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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
FBXO24 ENST00000427939 28.54 35.10 29.99 1.16 0.76 0.85 1.53 1.58 1.46
KBTBD7 ENST00000379483 28.55 49.24 37.12 1.15 0.66 0.81 1.53 2.02 1.95
ZBTB24 ENST00000230122 28.55 33.79 29.35 1.16 0.85 0.84 1.53 1.55 1.35
MTFR1L ENST00000374301 28.56 34.15 29.54 1.16 0.84 0.84 1.53 1.55 1.38
TSHR ENST00000541158 28.56 68.03 47.02 1.16 0.52 0.70 1.53 1.18 1.88
RAB23 ENST00000317483 28.57 44.54 34.76 1.16 0.65 0.90 1.53 1.97 1.76
UNC13B ENST00000378495 28.57 29.78 27.31 1.16 1.13 0.97 1.53 1.40 1.24
SHE ENST00000304760 28.58 10.98 17.69 1.16 2.09 1.68 1.53 0.52 0.78
PSMB1 ENST00000262193 28.58 10.88 17.56 1.16 2.11 1.63 1.53 0.50 0.76
IST1 ENST00000535424 28.59 36.53 30.82 1.16 0.78 0.78 1.54 1.63 1.49
KCNS1 ENST00000306117 28.59 35.07 30.02 1.16 0.76 0.81 1.54 1.58 1.45
FAM69A ENST00000370310 28.60 19.14 21.97 1.16 1.49 1.19 1.54 0.76 0.96
NUBPL ENST00000281081 28.60 51.34 38.27 1.16 0.63 0.85 1.54 1.90 2.04
NFATC3 ENST00000346183 28.61 10.09 17.19 1.16 2.33 1.64 1.54 0.49 0.73
MARCH7 ENST00000259050 28.61 15.34 20.00 1.16 1.89 1.49 1.54 0.67 0.85
GPT2 ENST00000340124 28.62 35.30 30.15 1.16 0.76 0.81 1.54 1.58 1.46
SLC35B1 ENST00000240333 28.62 58.97 42.02 1.16 0.52 0.70 1.54 1.42 1.99
BNC1 ENST00000345382 28.63 13.80 19.20 1.16 2.06 1.53 1.54 0.60 0.85
SLC17A2 ENST00000360488 28.63 48.48 36.75 1.16 0.65 0.82 1.54 2.02 1.94
ARL6 ENST00000463745 28.64 41.62 33.28 1.16 0.62 0.87 1.55 1.81 1.70
ELP3 ENST00000256398 28.65 54.22 39.79 1.16 0.62 0.80 1.55 1.71 2.02
HINFP ENST00000350777 28.65 26.88 25.93 1.16 1.23 1.01 1.55 1.12 1.24
REM2 ENST00000267396 28.66 73.09 49.84 1.16 0.53 0.65 1.55 1.02 1.89
BBS7 ENST00000264499 28.66 38.28 31.68 1.16 0.75 0.89 1.55 1.71 1.59
MOG ENST00000376898 28.67 33.11 29.05 1.16 0.82 0.82 1.55 1.50 1.32

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