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C2ORF15 vs C2orf15 #329

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blajoie opened this issue Feb 28, 2018 · 1 comment
Open

C2ORF15 vs C2orf15 #329

blajoie opened this issue Feb 28, 2018 · 1 comment

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@blajoie
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blajoie commented Feb 28, 2018

We (@vgainullin) have found an occurrence of case-sensitive gene names?

http://exac.broadinstitute.org/gene/ENSG00000273045
http://exac.broadinstitute.org/gene/ENSG00000241962

Both of these GENES exist in the fordist_cleaned_exac_r03_march16_z_pli_rec_null_data.txt.gz dump.

C2ORF15 looks to be invalid. Perhaps this is a bug?
Affecting GNOMAD as well?

{ u'bp': 378,
u'cds_end': 99767297,
u'cds_start': 99763930,
u'chr': u'2',
u'exp_lof': 4.02128738,
u'exp_mis': 31.9587584,
u'exp_syn': 12.886011,
u'gene': u'C2ORF15',
u'lof_z': 0.50449294,
u'mis_z': 0.34251584,
u'mu_lof': 2.8e-07,
u'mu_mis': 2.75e-06,
u'mu_syn': 1.06e-06,
u'n_exons': 2,
u'n_lof': 3,
u'n_mis': 28,
u'n_syn': 14,
u'pLI': 0.01311959,
u'pNull': 0.3262246,
u'pRec': 0.66065581,
u'syn_z': -0.19238513,
u'transcript': u'ENST00000302513.2'}

{ u'bp': 486,
u'cds_end': 99812168,
u'cds_start': 99802666,
u'chr': u'2',
u'exp_lof': 6.23037702,
u'exp_mis': 48.13188456,
u'exp_syn': 18.57931905,
u'gene': u'C2orf15',
u'lof_z': 2.0757045,
u'mis_z': -0.41371287,
u'mu_lof': 3.9e-07,
u'mu_mis': 4.24e-06,
u'mu_syn': 1.5e-06,
u'n_exons': 5,
u'n_lof': 1,
u'n_mis': 54,
u'n_syn': 15,
u'pLI': 0.54325245,
u'pNull': 0.01430108,
u'pRec': 0.44244647,
u'syn_z': 0.5147959,
u'transcript': u'ENST00000512183.2'}

@tayaza
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tayaza commented Mar 11, 2019

Seems the problem is from the annotation from GENCODE starting from version 19. It would be great to confirm if these are two different ORFs (as suggested by the Ensembl Ids) or if they're isoforms of the same thing.

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