Adding conflicting evidence to FRA12A_DIP2B

data/STRchive-loci.json

@@ -1576,7 +1576,7 @@
   "id": "FRA12A_DIP2B",
   "disease_id": "FRA12A",
   "gene": "DIP2B",
-  "evidence": ["Moderate"],
+  "evidence": ["Disputed"],
   "chrom": "chr12",
   "start_hg38": 50505001,
   "stop_hg38": 50505024,

data/criTRia-curations.json

@@ -1989,7 +1989,7 @@
   "Description": "FRA12A is a rare, folate-sensitive chromosomal fragile site on chromosome 12 associated with intellectual developmental disorder, FRA12A type. The DIP2B CGG repeat expansion causes this folate-sensitive site and is associated with a broad phenotypic range, including intellectual disability, ataxia/movement disorder, and epilepsy; cardiovascular associations have also been reported but were not scored and are noted for completeness. For this curation, the neurodevelopmental and neurologic presentations (intellectual disability, ataxia/movement disorder, and epilepsy) were lumped as a single phenotypic spectrum, which supports the current score. If these phenotypes are treated as distinct entities, the evidence strength and resulting score may differ. Patients across multiple independent families and cohorts provide inheritance and functional support. Mechanistically, repeat expansions are associated with promoter hypermethylation, altered regulatory activity, and changes in DIP2B expression. Case-control studies report enrichment of DIP2B expansions in ataxia cohorts (OR = 2.8) and cardiovascular disease populations (OR = 2.7), and computational analyses support biological relevance through conservation and a predicted interaction with the DMAP1 methylation complex.",
   "Source": "criTRia",
   "SOP_version": "criTRia v0",
-  "Manual_evidence_level": null,
+  "Manual_evidence_level": "Disputed",
   "genetic_evidence_details": [
   {
     "Evidence type": "Probands",
@@ -2002,6 +2002,17 @@
     "category_max_score": 6,
     "publication_dates": ["2025-03-01", "2007-02-01", "2021-01-01"]
   },
+  {
+    "Evidence type": "Allele",
+    "Score": 0.0,
+    "Citation": "pmid:42205056",
+    "Evidence detail": "A cohort of 14 probands with expanded alleles identified no common phenotypic pattern. This included healthy probands with highly expanded alleles, and probands with various neurological and non neurological presentations. There was no clear association between size of expanded alleles and presence of neurological disorders, which contributes to the disputed classification of this locus.",
+    "evidence_category": "Collective Evidence",
+    "evidence_supercategory": "Genetic Evidence",
+    "evidence_max_score": 2,
+    "category_max_score": 3,
+    "publication_dates": ["2026-05-28"]
+  },
   {
     "Evidence type": "Computational",
     "Score": 0.5,
@@ -2027,14 +2038,14 @@
   "experimental_evidence_details": [
   {
     "Evidence type": "Regulatory impact",
-    "Score": 1.0,
-    "Citation": "pmid:37248219",
-    "Evidence detail": "Repeat expansion associated with promoter hypermethylation, loss of regulatory activity, and predicted allelic silencing. Expanded CGG repeat associated with promoter methylation and reduced DIP2B expression. Unmethylated expansion associated with overexpression.",
+    "Score": 0.5,
+    "Citation": "pmid:37248219; pmid:42205056",
+    "Evidence detail": "Repeat expansion associated with loss of regulatory activity, and predicted allelic silencing. Hypermethylation has been detected in expanded alleles, however another correlation analysis of long-read genomes shows no strong association between DIP2B CGG repeat length and promoter hypermethylation. Expanded CGG repeat associated with reduced DIP2B expression. Unmethylated expansion associated with overexpression.",
     "evidence_category": "Function",
     "evidence_supercategory": "Experimental Evidence",
     "evidence_max_score": 2,
     "category_max_score": 2,
-    "publication_dates": ["2023-05-29"]
+    "publication_dates": ["2023-05-29", "2026-05-28"]
   },
   {
     "Evidence type": "Patient cells",
@@ -2052,20 +2063,20 @@
     "Singular Evidence": 6.0,
     "Collective Evidence": 0.5,
     "Statistics": 3.0,
-    "Function": 1.0,
+    "Function": 0.5,
     "Functional Alteration": 0.5,
     "Models": 0,
     "Rescue": 0
   },
   "supercategory_summary":
   {
-    "Experimental Evidence": 1.5,
+    "Experimental Evidence": 1.0,
     "Genetic Evidence": 9.5
   },
-  "total_score": 11.0,
-  "publication_count": 5,
-  "publication_interval_years": 18.08,
-  "classification": "Moderate"
+  "total_score": 10.5,
+  "publication_count": 6,
+  "publication_interval_years": 19.32,
+  "classification": "Disputed"
 },
 {
   "Disease_ID": "DMD",