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data/STRchive-loci.json
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| "webstr_hg38": [], | ||
| "webstr_hg19": [], | ||
| "tr_atlas": [], | ||
| "disease_description": "CPUM is characterized by progressive widespread hyperpigmentation beginning at birth without accompanying symptoms. Studied children with CPUM have been born to unaffected parents [@doi:10.3892/br.2025.2016].", |
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Could maybe add the age that the children were followed until in the paper since they haven't reached adulthood without additional symptoms yet. Maybe also if the phenotype differs from other types of hyperpigmentation.
data/STRchive-loci.json
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| "mechanism": "LoF", | ||
| "mechanism_detail": "Proposed mechanism involves repeat expansions in non-coding regions of the gene, reducing expression in melanocytes or keratinocytes, leading to a disruption in nucleotide balance in DNA repair and hyperpigmentation [@doi:10.3892/br.2025.2016].", | ||
| "source": [], | ||
| "details": "Missense mutations disrupt nucleotide metabolsim, resulting in loss-of-function and genome instability [@doi:10.3892/br.2025.2016].", |
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This information in details seems to belong in the mechanism_detail section. Here you could include some information about the tandem repeat itself. For example the information used to estimate the benign and pathogenic ranges and that the parents were heterozygous.
Edited the disease description and details.
hdashnow
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This is great, thanks!
A few more suggestions
| "mechanism_detail": "Proposed mechanism involves repeat expansions in non-coding regions of the gene, reducing expression in melanocytes or keratinocytes, leading to a disruption in nucleotide balance in DNA repair and hyperpigmentation. Missense mutations disrupt nucleotide metabolsim, resulting in loss-of-function and genome instability [@doi:10.3892/br.2025.2016].", | ||
| "source": [], | ||
| "details": "Missense mutations disrupt nucleotide metabolsim, resulting in loss-of-function and genome instability [@doi:10.3892/br.2025.2016].", | ||
| "details": "A study has identified an intronic GATGGT hexanucleotide tandem repeat in the TYMS gene. Both parents were found to be heterozygous carriers of the expansion, suggesting a recessive inheritance pattern [@doi:10.3892/br.2025.2016].", |
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One more request. I think it needs to be made clear that there is limited evidence. I suggest adding that:
Only a single family with two monozygotic twin probands has been reported.
No change in expression of the gene has been observed so the variant has yet to be biochemically confirmed as the causal variant. Or something along those lines.
| "webstr_hg19": [], | ||
| "tr_atlas": [], | ||
| "disease_description": "CPUM is characterized by progressive widespread hyperpigmentation beginning at birth without accompanying symptoms. Studied children with CPUM have been born to unaffected parents [@doi:10.3892/br.2025.2016].", | ||
| "disease_description": "CPUM is characterized by progressive widespread hyperpigmentation beginning at birth without accompanying symptoms. Studied children with CPUM have been born to unaffected parents. The children studied have been born with diffuse, universal, and progressive hyperpigmentaion at 15 years of age. At this time the hyperpigmentation had fully progressed [@doi:10.3892/br.2025.2016].", |
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May or may not be a new disease as shared phenotype features with ....
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Closing in favour of #212 |
## Description This is the same content as in #204 by @Macayla-weiner, except I've rebased it against main so that it should include a better website preview, including properly formatted references. Replaces: #204 Fixes: #200 ## Major Changes - New locus: CPUM_TYMS ## Checklist - [x] All changes are well summarized - [x] Check all tests pass - [x] Check that the website preview looks good - [ ] Update the STRchive version in `CITATION.cff`, format X.Y.Z. If any major changes, increment Y. If only minor changes, increment Z. If the breaking change (rare), increment X. - [x] Ask someone to review this PR --------- Co-authored-by: Macayla Ann Weiner <macanncash@gmail.com> Co-authored-by: hdashnow <3794821+hdashnow@users.noreply.github.com>
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Description
Summarize the changes
Added CPUM_TYMS locus to the json
Fixes: #200
Major Changes
Checklist
CITATION.cff, format X.Y.Z. If any major changes, increment Y. If only minor changes, increment Z. If the breaking change (rare), increment X.