|
46 | 46 | "prevalence": null, |
47 | 47 | "prevalence_details": "Found in individuals of European, Japanese, and Chinese ancestry [@pmid:38876750; @pmid:34047774].", |
48 | 48 | "stripy": [], |
49 | | - "gnomad": [], |
| 49 | + "gnomad": ["ABCD3"], |
50 | 50 | "genereviews": [], |
51 | 51 | "mondo": ["0025193"], |
52 | 52 | "year": "2023 [@pmid:39068203]", |
|
174 | 174 | "prevalence": null, |
175 | 175 | "prevalence_details": "1/862 (1/654-1266) population prevalence of methylated AFF3 expansions (mild cognitive disability) [@pmid:39313615]. Disease cases observed in South Australia [@pmid:24763282].", |
176 | 176 | "stripy": [], |
177 | | - "gnomad": [], |
| 177 | + "gnomad": ["AFF3"], |
178 | 178 | "genereviews": [], |
179 | 179 | "mondo": [], |
180 | 180 | "year": "2014 [@pmid:24763282]", |
|
1070 | 1070 | "prevalence": null, |
1071 | 1071 | "prevalence_details": "1/100,000 births; female/male ratio 2:1 [@pmid:19267933]. Found across ancestries/ethnicities [@omim:147791].", |
1072 | 1072 | "stripy": ["CBL"], |
1073 | | - "gnomad": [], |
| 1073 | + "gnomad": ["CBL"], |
1074 | 1074 | "genereviews": [], |
1075 | 1075 | "mondo": ["0007838"], |
1076 | 1076 | "year": "1995 [@pmid:7603564]", |
|
1242 | 1242 | "location_in_gene": null, |
1243 | 1243 | "benign_min": 2.0, |
1244 | 1244 | "benign_max": 3.0, |
1245 | | - "intermediate_min": 12.0, |
1246 | | - "intermediate_max": 17.0, |
| 1245 | + "intermediate_min": null, |
| 1246 | + "intermediate_max": null, |
1247 | 1247 | "pathogenic_min": 30.0, |
1248 | | - "pathogenic_max": 81.0, |
| 1248 | + "pathogenic_max": 125.0, |
1249 | 1249 | "ref_copies": null, |
1250 | 1250 | "motif_len": 12, |
1251 | 1251 | "age_onset": "Typical: 6-15 [@genereviews:NBK1142]; Range: 6-18 [@pmid:18325013].", |
|
1255 | 1255 | "typ_age_onset_max": 15.0, |
1256 | 1256 | "novel": null, |
1257 | 1257 | "mechanism": "LoF", |
1258 | | - "mechanism_detail": "LoF [@pmid:38467784].", |
| 1258 | + "mechanism_detail": "The repeat expanison causes significantly reduced expression of cystatin-B protein [@genereviews:NBK1142].", |
1259 | 1259 | "source": [], |
1260 | | - "details": null, |
| 1260 | + "details": "Affected individuals have an unstable 12-nucleotide (dodecomer) repeat expansion. Alleles containing 2-3 motifs are considered benign, while alleles with 30-125 repeats are fully penetrant [@pmid:18325013]. Alleles in the range 12-17 repeats have been observed, however the individuals carrying them have not undergone clinical evaluation. Alleles in the range 4-11 and 18-29 repeats have not been reported to date.", |
1261 | 1261 | "omim": ["254800"], |
1262 | 1262 | "prevalence": null, |
1263 | 1263 | "prevalence_details": "Worldwide prevalence unknown; Finland prevalence 2-4/100,000. Found across ethnicities/ancestries, with population-dependent prevalence; highest in Tunisia, Algeria, Morocco, and Finland [@genereviews:NBK1142].", |
|
1646 | 1646 | "prevalence": null, |
1647 | 1647 | "prevalence_details": "Intermediate expansions 1-2% of population, but non-GAA-pure without relation to ataxia [@genereviews:NBK599589]. Found in multiple ethnicities [@pmid:38876750]; diagnosed patients in America, Brazil, Japan, Germany, Spain, Canada, France, Austria, Australia, and Italy [@genereviews:NBK599589; @pmid:38886208; @pmid:37267898].", |
1648 | 1648 | "stripy": ["FGF14"], |
1649 | | - "gnomad": [], |
| 1649 | + "gnomad": ["FGF14"], |
1650 | 1650 | "genereviews": ["NBK599589"], |
1651 | 1651 | "mondo": ["0859340"], |
1652 | 1652 | "year": "2023 [@pmid:36493768]", |
|
2267 | 2267 | "benign_min": 6.0, |
2268 | 2268 | "benign_max": 26.0, |
2269 | 2269 | "intermediate_min": 27.0, |
2270 | | - "intermediate_max": 39.0, |
2271 | | - "pathogenic_min": 40.0, |
| 2270 | + "intermediate_max": 35.0, |
| 2271 | + "pathogenic_min": 36.0, |
2272 | 2272 | "pathogenic_max": 250.0, |
2273 | 2273 | "ref_copies": 21.3, |
2274 | 2274 | "motif_len": 3, |
|
2281 | 2281 | "mechanism": "GoF/LoF", |
2282 | 2282 | "mechanism_detail": "While the primary pathogenic mechanism is gain of function of the protein product, pathogenesis is complex and multifactorial [@pmid:27940602].", |
2283 | 2283 | "source": [], |
2284 | | - "details": "27-35 motifs are unstable/premutations, while 36-39 motifs are associated with reduced penetrance and mild phenotypes [@pmid:39572770]. >60 motifs associated with onset age <20 years [@genereviews:NBK1305]. Only CAG expansions are considered pathogenic, but interruptions impact pathogenicity (e.g. CAA) [@pmid:35245110]. Only fathers with premutations are considered at risk of transmitting pathogenic alleles [@pmid:19507258]. CAG repeats in the non-HD range (>= 21 repeats) may modulate psychiatric disease risk in an age-dependent manner [@pmid:39572770]", |
| 2284 | + "details": "27-35 motifs are unstable/premutations, while 36-39 motifs are associated with reduced penetrance and mild phenotypes [@pmid:39572770], and alleles over 40 repeats are typically fully penetrant [@genereviews:NBK1305]. >60 motifs associated with onset age <20 years [@genereviews:NBK1305]. Only CAG expansions are considered pathogenic, but interruptions impact pathogenicity (e.g. CAA) [@pmid:35245110]. Only fathers with premutations are considered at risk of transmitting pathogenic alleles [@pmid:19507258]. CAG repeats in the non-HD range (>= 21 repeats) may modulate psychiatric disease risk in an age-dependent manner [@pmid:39572770]", |
2285 | 2285 | "omim": ["143100"], |
2286 | 2286 | "prevalence": "1/10000", |
2287 | 2287 | "prevalence_details": "6.5-15/100,000 [@pmid:29100084]. 9.71-17:100,000 (European) vs. 0.1-2/100,000 (African), as many as 1 in 400 have reduced penetrance (0.2-2% for 36-38 CAG) HTT alleles [@genereviews:NBK1305]. Found across ethnicities/ancestries, with population-dependent prevalence [@genereviews:NBK1305].", |
|
2606 | 2606 | "prevalence": null, |
2607 | 2607 | "prevalence_details": "Single proband found in Japanese cohort [@pmid:39455596].", |
2608 | 2608 | "stripy": [], |
2609 | | - "gnomad": [], |
| 2609 | + "gnomad": ["NAXE"], |
2610 | 2610 | "genereviews": [], |
2611 | 2611 | "mondo": ["0020781"], |
2612 | 2612 | "year": "2024 [@pmid:39455596]", |
|
3566 | 3566 | "prevalence": null, |
3567 | 3567 | "prevalence_details": "Population dependent: 21.6% of one OPDM cohort [@pmid:35148830]. Typically found in individuals of East Asian ancestry [@pmid:38876750].", |
3568 | 3568 | "stripy": ["RILPL1"], |
3569 | | - "gnomad": [], |
| 3569 | + "gnomad": ["RILPL1"], |
3570 | 3570 | "genereviews": [], |
3571 | 3571 | "mondo": ["0030712"], |
3572 | 3572 | "year": "2022 [@pmid:35148830]", |
|
4142 | 4142 | "prevalence": null, |
4143 | 4143 | "prevalence_details": "Has been observed in Chinese families [@pmid:37148549; @pmid:24677642]. Interruptions predisposing to expansion/disease appear to vary by ancestry [@pmid:39651830].", |
4144 | 4144 | "stripy": [], |
4145 | | - "gnomad": [], |
| 4145 | + "gnomad": ["THAP11"], |
4146 | 4146 | "genereviews": [], |
4147 | 4147 | "mondo": [], |
4148 | 4148 | "year": "2023 [@pmid:37148549]", |
|
4526 | 4526 | "prevalence": null, |
4527 | 4527 | "prevalence_details": "Observed in Swedish individuals: 2 original kindreds and 3 additional families [@omim:600223]; common ancestral allele has been identified [@pmid:39635987].", |
4528 | 4528 | "stripy": [], |
4529 | | - "gnomad": [], |
| 4529 | + "gnomad": ["ZFHX3"], |
4530 | 4530 | "genereviews": [], |
4531 | 4531 | "mondo": ["0010847"], |
4532 | 4532 | "year": "2023 [@pmid:38035881]", |
|
4718 | 4718 | "prevalence": null, |
4719 | 4719 | "prevalence_details": "1 proband reported alongside 3 individuals with premutations, found in 2 families without discussion of ancestry/ethnicity [@pmid:25196122].", |
4720 | 4720 | "stripy": [], |
4721 | | - "gnomad": [], |
| 4721 | + "gnomad": ["ZNF713"], |
4722 | 4722 | "genereviews": [], |
4723 | 4723 | "mondo": [], |
4724 | 4724 | "year": "2014 [@pmid:25196122]", |
|
4782 | 4782 | "prevalence": null, |
4783 | 4783 | "prevalence_details": "Found in 12 families, with ancestry including: Irish, White European, French (Normandie), Ashkenazi, French Canadian, Danish/White European, Welsh, Scottish, Italian, British/White European, Italian/Turkish/Lebanese, German/Palestinian, and South Chinese [@pmid:38714868].", |
4784 | 4784 | "stripy": [], |
4785 | | - "gnomad": [], |
| 4785 | + "gnomad": ["PRE-MIR7-2"], |
4786 | 4786 | "genereviews": [], |
4787 | 4787 | "mondo": ["0012360"], |
4788 | 4788 | "year": "2024 [@pmid:38714869]", |
|
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