July lit update (#248)

Macayla-weiner · hdashnow · web-flow · commit 141dffb5ba8b · 2025-08-12T12:23:23.000-06:00
## Description

July lit update presented a proposed correlation between ATXN2 and
SCA3-related ALS risks. Another PLIN4 paper was published, giving
pathogenic range, age onset, and ancestry details.

Fixes: # N/A

## Major Changes

- PLIN4 pathogenic min decreased from 39 to 37

## Minor Changes

- Minor update to SCA3
- PLIN4 pathogenic min, age onset upper bound, and ancestry details
updated
- FRDA description updated

## Checklist

- [x] All changes are well summarized
- [x] Check all tests pass
- [x] Check that the website preview looks good
- [x] 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: Harriet Dashnow &lt;h.dashnow@gmail.com&gt;
Co-authored-by: hdashnow &lt;3794821+hdashnow@users.noreply.github.com&gt;
diff --git a/CITATION.cff b/CITATION.cff
@@ -1,6 +1,6 @@
 title: STRchive
-version: 2.8.0
-date-released: "2025-08-08"
+version: 2.9.0
+date-released: "2025-08-12"
 url: https://github.com/dashnowlab/STRchive
 authors:
   - family-names: Dashnow
diff --git a/data/STRchive-citations.json b/data/STRchive-citations.json
diff --git a/data/STRchive-disease-loci.T2T-chm13.bed b/data/STRchive-disease-loci.T2T-chm13.bed
@@ -55,7 +55,7 @@ chr17	17754961	17755053	FAME8_RAI1	RAI1	TTTTA	TTTCA	9	AD	Familial adult myocloni
 chr17	81047404	81047534	RCPS_EIF4A3	EIF4A3	CCTCGCTGTGCCGCTGCCGA	CCTCGCTGTGCCGCTGCCGA	14	AR	Richieri-Costa-Pereira syndrome
 chr18	821235	821905	CPUM_TYMS	TYMS	GATGGT	GATGGT	210	AR	Congenital Progressive Universal Melanosis
 chr18	55789233	55789288	FECD3_TCF4	TCF4	CAG	CAG	51	AD	Fuchs endothelial corneal dystrophy 3
-chr19	4494212	4497342	MRUPAV_PLIN4	PLIN4	TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC	TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC	39	AD	Myopathy with Rimmed Ubiquitin-Positive Autophagic Vacuolation, PLIN4-Related Myopathy
+chr19	4494212	4497342	MRUPAV_PLIN4	PLIN4	TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC	TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC	37	AD	Myopathy with Rimmed Ubiquitin-Positive Autophagic Vacuolation, PLIN4-Related Myopathy
 chr19	13333136	13333176	SCA6_CACNA1A	CACNA1A	CTG	CTG	21	AD	Spinocerebellar ataxia type 6
 chr19	14622655	14622692	OPDM2_GIPC1	GIPC1	CCG	CCG	73	AD	Oculopharyngodistal myopathy type 2
 chr19	18921630	18921645	EDM1-PSACH_COMP	COMP	GTC	GTC	6	AD	Multiple epiphyseal dysplasia, Pseudoachondroplasia
diff --git a/data/STRchive-disease-loci.hg19.bed b/data/STRchive-disease-loci.hg19.bed
@@ -55,7 +55,7 @@ chr17	17711672	17711774	FAME8_RAI1	RAI1	TTTTA	TTTCA	9	AD	Familial adult myocloni
 chr17	78120808	78120938	RCPS_EIF4A3	EIF4A3	CCTCGCTGTGCCGCTGCCGA	CCTCGCTGTGCCGCTGCCGA	14	AR	Richieri-Costa-Pereira syndrome
 chr18	666891	667632	CPUM_TYMS	TYMS	GATGGT	GATGGT	210	AR	Congenital Progressive Universal Melanosis
 chr18	53253384	53253460	FECD3_TCF4	TCF4	CAG	CAG	51	AD	Fuchs endothelial corneal dystrophy 3
-chr19	4510739	4513671	MRUPAV_PLIN4	PLIN4	TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC	TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC	39	AD	Myopathy with Rimmed Ubiquitin-Positive Autophagic Vacuolation, PLIN4-Related Myopathy
+chr19	4510739	4513671	MRUPAV_PLIN4	PLIN4	TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC	TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC	37	AD	Myopathy with Rimmed Ubiquitin-Positive Autophagic Vacuolation, PLIN4-Related Myopathy
 chr19	13318672	13318712	SCA6_CACNA1A	CACNA1A	CTG	CTG	21	AD	Spinocerebellar ataxia type 6
 chr19	14606853	14606887	OPDM2_GIPC1	GIPC1	CCG	CCG	73	AD	Oculopharyngodistal myopathy type 2
 chr19	18896844	18896860	EDM1-PSACH_COMP	COMP	GTC	GTC	6	AD	Multiple epiphyseal dysplasia, Pseudoachondroplasia
diff --git a/data/STRchive-disease-loci.hg38.bed b/data/STRchive-disease-loci.hg38.bed
@@ -55,7 +55,7 @@ chr17	17808358	17808460	FAME8_RAI1	RAI1	TTTTA	TTTCA	9	AD	Familial adult myocloni
 chr17	80147009	80147139	RCPS_EIF4A3	EIF4A3	CCTCGCTGTGCCGCTGCCGA	CCTCGCTGTGCCGCTGCCGA	14	AR	Richieri-Costa-Pereira syndrome
 chr18	666891	667632	CPUM_TYMS	TYMS	GATGGT	GATGGT	210	AR	Congenital Progressive Universal Melanosis
 chr18	55586153	55586229	FECD3_TCF4	TCF4	CAG	CAG	51	AD	Fuchs endothelial corneal dystrophy 3
-chr19	4510727	4513659	MRUPAV_PLIN4	PLIN4	TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC	TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC	39	AD	Myopathy with Rimmed Ubiquitin-Positive Autophagic Vacuolation, PLIN4-Related Myopathy
+chr19	4510727	4513659	MRUPAV_PLIN4	PLIN4	TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC	TGGTGTCCACGCCGGTCTGGATGGTTCCTTTGGCCACATTCATGGCACCAGTCACCCCACTACAGACGGTGTCCTTGGTACCTGTTAGGACAGTCTTAC	37	AD	Myopathy with Rimmed Ubiquitin-Positive Autophagic Vacuolation, PLIN4-Related Myopathy
 chr19	13207858	13207898	SCA6_CACNA1A	CACNA1A	CTG	CTG	21	AD	Spinocerebellar ataxia type 6
 chr19	14496041	14496075	OPDM2_GIPC1	GIPC1	CCG	CCG	73	AD	Oculopharyngodistal myopathy type 2
 chr19	18786034	18786050	EDM1-PSACH_COMP	COMP	GTC	GTC	6	AD	Multiple epiphyseal dysplasia, Pseudoachondroplasia
diff --git a/data/STRchive-loci.json b/data/STRchive-loci.json
@@ -295,7 +295,7 @@
   "typ_age_onset_max": 0.0,
   "novel": "ref",
   "mechanism": "LoF",
-  "mechanism_detail": "Polyalanine expansions lead to reduction in protein product through unclear mechanism [@pmid:36169768; @pmid:38467784]. Apparent aggregation and mis-localisation of mutan protein, increased with expansion length [@genereviews:NBK51932].",
+  "mechanism_detail": "Polyalanine expansions lead to reduction in protein product through unclear mechanism [@pmid:36169768; @pmid:38467784]. Apparent aggregation and mis-localisation of mutant protein, increased with expansion length [@genereviews:NBK51932].",
   "source": [],
   "details": "ARX expansions [@genereviews:NBK535148] result in a phenotypic spectrum of conditions including Partington syndrome [@omim:309510], Early Infantile Epileptic Encephalopathy [@omim:308350], Agenesis of Corpus Callosum with Abnormal Genitalia [@omim:300004], and X-Linked Lissencephaly with Ambiguous Genitalia [@omim:300215], described in the literature [@pmid:26029707; @pmid:20506206].",
   "omim": ["308350", "300419", "300215"],
@@ -697,7 +697,7 @@
   "webstr_hg38": ["5316666", "1481402"],
   "webstr_hg19": ["Expansion_SCA3_MJD/ATXN3"],
   "tr_atlas": ["TR132758"],
-  "disease_description": "Spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph disease, is the most common subtype of type 1 autosomal dominant cerebellar ataxia (ADCA type 1), a neurodegenerative disorder, and is characterized by ataxia, external progressive ophthalmoplegia, and other neurological manifestations [@mondo:0007182].",
+  "disease_description": "Spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph disease, is the most common subtype of type 1 autosomal dominant cerebellar ataxia (ADCA type 1), a neurodegenerative disorder, and is characterized by ataxia, external progressive ophthalmoplegia, and other neurological manifestations [@mondo:0007182]. Research suggests that length of ATXN2 expansions may affect the phenotype of SCA3 [@pmid:40684213].",
   "locus_tags": ["supported_evidence", "somatic_instability", "anticipation", "paternal_expansion", "maternal_expansion", "length_affects_onset", "length_affects_phenotype", "length_affects_severity"],
   "disease_tags": ["spinocerebellar_ataxia"],
   "references": ["genereviews:NBK1196", "pmid:40004498", "pmid:30414314", "pmid:36169768", "pmid:37906407", "pmid:35245110", "pmid:39731318", "pmid:39699045", "pmid:29100084", "genereviews:NBK557816", "pmid:7874163", "mondo:0007182"],
@@ -1577,7 +1577,7 @@
   "mechanism": "LoF",
   "mechanism_detail": "LoF from a hypomorphic allele [@pmid:24360810].",
   "source": [],
-  "details": "Complex repeat of 18-20 nucleotides expands to cause diease: disease is found in individuals with 14-16 repeats [@pmid:24360810], while controls have typically 3-12 repeats with as low as 1 repeat [@genereviews:NBK535148; @gnomad:EIF4A3]. Significance of intermediate alleles is unknown [@pmid:29112243].",
+  "details": "Complex repeat of 18-20 nucleotides expands to cause disease: disease is found in individuals with 14-16 repeats [@pmid:24360810], while controls have typically 3-12 repeats with as low as 1 repeat [@genereviews:NBK535148; @gnomad:EIF4A3]. Significance of intermediate alleles is unknown [@pmid:29112243].",
   "omim": ["268305"],
   "prevalence": null,
   "prevalence_details": "49 cases as of Nov 2023 [@doi:10.1016/j.omsc.2023.100340]. Found in Brazilian families and one unrelated French patient [@mondo:0009998].",
@@ -1849,7 +1849,7 @@
   "webstr_hg38": ["1509872"],
   "webstr_hg19": [],
   "tr_atlas": ["TR93516"],
-  "disease_description": "Any Friedreich ataxia in which the cause of the disease is a mutation in the FXN gene [@mondo:0100340].",
+  "disease_description": "Friedreich ataxia (FRDA) is an autosomal recessive neurodegenerative disorder characterized by progressive gait and limb ataxia with associated limb muscle weakness, absent lower limb reflexes, extensor plantar responses, dysarthria, and decreased vibratory sense and proprioception. Onset is usually in the first or second decade, before the end of puberty [@omim:229300].",
   "locus_tags": ["supported_evidence", "somatic_instability", "maternal_expansion", "length_affects_onset", "length_affects_phenotype", "motif_affects_instability", "motif_affects_onset", "motif_affects_penetrance"],
   "disease_tags": ["ataxia"],
   "references": ["genereviews:NBK1281", "pmid:16205714", "pmid:36169768", "pmid:11748752", "pmid:8815938", "omim:229300", "pmid:29100084", "pmid:8596916", "mondo:0100340"],
@@ -3100,13 +3100,13 @@
   "benign_max": 31.0,
   "intermediate_min": null,
   "intermediate_max": null,
-  "pathogenic_min": 39.0,
+  "pathogenic_min": 37.0,
   "pathogenic_max": 50.0,
   "ref_copies": 31.0,
   "motif_len": 99,
-  "age_onset": "22-65 [@pmid:36151849; @pmid:37145156; @pmid:35499779].",
+  "age_onset": "22-66 [@pmid:36151849; @pmid:37145156; @pmid:35499779; @pmid:40693562].",
   "age_onset_min": 22,
-  "age_onset_max": 65,
+  "age_onset_max": 66,
   "typ_age_onset_min": null,
   "typ_age_onset_max": null,
   "novel": "ref",
@@ -3116,7 +3116,7 @@
   "details": "This is an expanded variable number tandem repeat (VNTR) in the PLIN4 gene, located in exon 3. This repeat consists of a 99 bp motif which encodes 33 amino-acids within the perilipin-4 protein [@pmid:32451610]. Expansions of this 99 bp motif leads to insertion of multiple imperfect 33–amino acid repeats. These repetitive sequences are thought to contribute to abnormal protein aggregation and dysregulated autophagy seen in affected muscle tissue [@omim:601846].",
   "omim": ["601846"],
   "prevalence": null,
-  "prevalence_details": "Studied in patients of chinese ancestry [@pmid:36151849].",
+  "prevalence_details": "Studied in patients of chinese ancestry and two families of spanish ancestry [@pmid:36151849; @pmid:40693562].",
   "stripy": [],
   "gnomad": [],
   "genereviews": [],
diff --git a/data/STRchive-loci.schema.json b/data/STRchive-loci.schema.json
@@ -36,7 +36,7 @@
         "type": [ "integer", "null" ]
       },
       "id": {
-        "description": "Unique identifier for the locus within STRchive in the form [disease_id]_[gene] e.g. CANVAS_RFC1",
+        "description": "Unique identifier for the locus within STRchive in the form [disease_id]_[gene] e.g. CANVAS_RFC1. Additional characters may be added to the end of the ID to make it unique within STRchive, e.g. HFG_HOXA13-I, HFG_HOXA13-II",
         "type": "string"
       },
       "disease_id": {
diff --git a/data/plots/age-onset.json b/data/plots/age-onset.json
@@ -12,7 +12,7 @@
     "offset": -0.1,
     "orientation": "h",
     "width": 0.2,
-    "x": [47, 32, 39, 52, 51, 43, 66, 71, 59, 0, 52, 19, 46, 57, 25, 56, 0, 53, 54, 72, 36, 23, 68, 40, 20, 75, 54, 60, 0, 61, 59, 57, 0, 0, 47, 56, 59, 10, 70, 84, 0, 0, 1, 84, 6, 0, 0, 73, 76, 72, 74, 0, 65, 0, 0, 3, 36, 0, 0],
+    "x": [47, 32, 39, 52, 51, 44, 66, 71, 59, 0, 52, 19, 46, 57, 25, 56, 0, 53, 54, 72, 36, 23, 68, 40, 20, 75, 54, 60, 0, 61, 59, 57, 0, 0, 47, 56, 59, 10, 70, 84, 0, 0, 1, 84, 6, 0, 0, 73, 76, 72, 74, 0, 65, 0, 0, 3, 36, 0, 0],
     "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "ADTKD", "FAME7", "SCA37", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLMR", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
     "type": "bar"
   },
diff --git a/data/plots/path-size.json b/data/plots/path-size.json
@@ -33,7 +33,7 @@
     "type": "bar"
   },
   {
-    "base": [5000, 4000, 3955, 3900, 3861, 3300, 2040, 2000, 1506, 1370, 1350, 1260, 1000, 960, 900, 819, 603, 603, 550, 525, 483, 360, 360, 354, 303, 300, 300, 280, 255, 219, 216, 213, 210, 198, 180, 177, 168, 155, 153, 153, 150, 147, 144, 138, 135, 120, 120, 117, 114, 111, 108, 105, 78, 75, 75, 66, 66, 66, 66, 63, 60, 60, 54, 54, 51, 45, 45, 36, 36, 33, 18, 12, 10, 0],
+    "base": [5000, 4000, 3955, 3900, 3663, 3300, 2040, 2000, 1506, 1370, 1350, 1260, 1000, 960, 900, 819, 603, 603, 550, 525, 483, 360, 360, 354, 303, 300, 300, 280, 255, 219, 216, 213, 210, 198, 180, 177, 168, 155, 153, 153, 150, 147, 144, 138, 135, 120, 120, 117, 114, 111, 108, 105, 78, 75, 75, 66, 66, 66, 66, 63, 60, 60, 54, 54, 51, 45, 45, 36, 36, 33, 18, 12, 10, 0],
     "hovertemplate": "Disease: %{y} \u003cbr\u003e Range: %{base} - %{x} bp",
     "legendgroup": "Pathogenic",
     "marker":
@@ -44,7 +44,7 @@
     "offset": -0.3,
     "orientation": "h",
     "width": 0.6,
-    "x": [0, 18500, 1220, 11100, 1089, 0, 2460, 11750, 23022, 1420, 0, 294, 0, 1851, 0, 99, 5397, 5397, 3250, 17875, 1617, 1140, 231, 1728, 597, 43700, 10700, 40, 612, 273, 114, 3687, 102, 1353, 81, 69, 4932, 220, 81, 7647, 11850, 51, 135, 84, 165, 60, 264, 156, 90, 1269, 642, 1395, 21, 0, 0, 0, 30, 3, 12, 36, 0, 21, 0, 3, 30, 27, 1625, 18, 0, 135, 3, 0, 20, 0],
+    "x": [0, 18500, 1220, 11100, 1287, 0, 2460, 11750, 23022, 1420, 0, 294, 0, 1851, 0, 99, 5397, 5397, 3250, 17875, 1617, 1140, 231, 1728, 597, 43700, 10700, 40, 612, 273, 114, 3687, 102, 1353, 81, 69, 4932, 220, 81, 7647, 11850, 51, 135, 84, 165, 60, 264, 156, 90, 1269, 642, 1395, 21, 0, 0, 0, 30, 3, 12, 36, 0, 21, 0, 3, 30, 27, 1625, 18, 0, 135, 3, 0, 20, 0],
     "y": ["FAME4", "SCA10", "FAME3", "SCA36", "MRUPAV", "FAME6", "GDPAG", "CANVAS", "FTDALS1", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "SCA31", "FAME1", "OPML1", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM2", "DBQD2, BSS", "SCA8", "XDP", "NIID", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLMR", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"],
     "type": "bar"
   },
@@ -96,7 +96,7 @@
     },
     "mode": "lines",
     "showlegend": false,
-    "x": [3069, 3861],
+    "x": [3069, 3663],
     "y": ["MRUPAV", "MRUPAV"],
     "type": "scatter"
   },
