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Add-CPUM.json #204

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Add-CPUM.json
Macayla-weiner Jun 25, 2025
3f7c804
CPUM-2.json
Macayla-weiner Jun 25, 2025
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CPUM-3json
Macayla-weiner Jun 25, 2025
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CPUM-4.json
Macayla-weiner Jun 26, 2025
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64 changes: 64 additions & 0 deletions data/STRchive-loci.json
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Original file line number Diff line number Diff line change
Expand Up @@ -4670,4 +4670,68 @@
"disease_tags": [],
"references": ["pmid:38714868", "pmid:38714869", "omim:609893"],
"additional_literature": []
},
{
"chrom": "chr18",
"start_hg38": 666891,
"stop_hg38": 667632,
"start_hg19": 666891,
"stop_hg19": 667632,
"start_t2t": 821216,
"stop_t2t": 821905,
"id": "CPUM_TYMS",
"disease_id": "CPUM",
"gene_strand": "-",
"reference_motif_reference_orientation": ["GATGGT"],
"pathogenic_motif_reference_orientation": ["GATGGT"],
"pathogenic_motif_gene_orientation": ["ACCATC"],
"benign_motif_reference_orientation": [],
"benign_motif_gene_orientation": [],
"unknown_motif_reference_orientation": [],
"unknown_motif_gene_orientation": [],
"disease": "Congenital Progressive Universal Melanosis",
"gene": "TYMS",
"flank_motif": null,
"locus_structure": "(GATGGT)*",
"inheritance": ["AR"],
"type": "Non-coding",
"location_in_gene": "Intron 3",
"benign_min": 42,
"benign_max": 172,
"intermediate_min": null,
"intermediate_max": null,
"pathogenic_min": 210,
"pathogenic_max": 259,
"ref_copies": null,
"motif_len": 6,
"age_onset": "0 (birth) [@doi:10.3892/br.2025.2016]",
"age_onset_min": 0.0,
"age_onset_max": 0.0,
"typ_age_onset_min": null,
"typ_age_onset_max": null,
"novel": "ref",
"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. Missense mutations disrupt nucleotide metabolsim, resulting in loss-of-function and genome instability [@doi:10.3892/br.2025.2016].",
"source": [],
"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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@hdashnow hdashnow Jun 26, 2025

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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.

"omim": [],
"prevalence": null,
"prevalence_details": "Found in two monozygotic twins in Thailand [@doi:10.3892/br.2025.2016].",
"stripy": [],
"gnomad": ["TYMS"],
"genereviews": [],
"mondo": [],
"year": "2025 [@doi:10.3892/br.2025.2016]",
"medgen": [],
"orphanet": [],
"gard": [],
"malacard": [],
"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. 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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@hdashnow hdashnow Jun 26, 2025

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May or may not be a new disease as shared phenotype features with ....

"locus_tags": ["sparse_evidence"],
"disease_tags": [],
"references": ["@doi:10.3892/br.2025.2016"],
"additional_literature": []
}]
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