From 98acd84d39ce42e3232289d123b5a97a16dd1cc3 Mon Sep 17 00:00:00 2001 From: Macayla Ann Weiner Date: Wed, 25 Jun 2025 09:39:53 -0600 Subject: [PATCH 1/4] Add-CPUM.json --- data/STRchive-loci.json | 64 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) diff --git a/data/STRchive-loci.json b/data/STRchive-loci.json index 27c55305..a63d3f58 100644 --- a/data/STRchive-loci.json +++ b/data/STRchive-loci.json @@ -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": null, + "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)", + "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 [@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].", + "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 [@doi:10.3892/br.2025.2016].", + "locus_tags": ["sparse_evidence"], + "disease_tags": [], + "references": [], + "additional_literature": [] }] From 3f7c80499e3b3e1cf353d44e696756695393afe7 Mon Sep 17 00:00:00 2001 From: Macayla Ann Weiner Date: Wed, 25 Jun 2025 09:54:17 -0600 Subject: [PATCH 2/4] CPUM-2.json --- data/STRchive-loci.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/STRchive-loci.json b/data/STRchive-loci.json index a63d3f58..29eb49ff 100644 --- a/data/STRchive-loci.json +++ b/data/STRchive-loci.json @@ -4711,7 +4711,7 @@ "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 [@doi:10.3892/br.2025.2016]", + "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].", "omim": [], From 76b61a1f421f517bf48f1831e4f16e55c63c7e4f Mon Sep 17 00:00:00 2001 From: Macayla Ann Weiner Date: Wed, 25 Jun 2025 10:18:11 -0600 Subject: [PATCH 3/4] CPUM-3json --- data/STRchive-loci.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/data/STRchive-loci.json b/data/STRchive-loci.json index 29eb49ff..0179b4a8 100644 --- a/data/STRchive-loci.json +++ b/data/STRchive-loci.json @@ -4692,7 +4692,7 @@ "disease": "Congenital Progressive Universal Melanosis", "gene": "TYMS", "flank_motif": null, - "locus_structure": null, + "locus_structure": "(GATGGT)*", "inheritance": ["AR"], "type": "Non-coding", "location_in_gene": "Intron 3", @@ -4704,7 +4704,7 @@ "pathogenic_max": 259, "ref_copies": null, "motif_len": 6, - "age_onset": "0 (birth)", + "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, @@ -4732,6 +4732,6 @@ "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].", "locus_tags": ["sparse_evidence"], "disease_tags": [], - "references": [], + "references": ["@doi:10.3892/br.2025.2016"], "additional_literature": [] }] From f513368c6ede504f82d60c4de518d34ab5f405a6 Mon Sep 17 00:00:00 2001 From: Macayla Ann Weiner Date: Wed, 25 Jun 2025 20:46:42 -0600 Subject: [PATCH 4/4] CPUM-4.json Edited the disease description and details. --- data/STRchive-loci.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/data/STRchive-loci.json b/data/STRchive-loci.json index 0179b4a8..7fcdeb59 100644 --- a/data/STRchive-loci.json +++ b/data/STRchive-loci.json @@ -4711,9 +4711,9 @@ "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 [@doi:10.3892/br.2025.2016].", + "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].", "omim": [], "prevalence": null, "prevalence_details": "Found in two monozygotic twins in Thailand [@doi:10.3892/br.2025.2016].", @@ -4729,7 +4729,7 @@ "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].", + "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].", "locus_tags": ["sparse_evidence"], "disease_tags": [], "references": ["@doi:10.3892/br.2025.2016"],