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| Early onset or syndromic epilepsy v7.84 | SAMD12_TTTCA |
Sarah Leigh changed review comment from: SAMD12 transcribed from the reverse strand, which means that the repeated sequence is the reverse compliment of the forward strand sequence. SAMD12_TTTCA is on https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r3 SAMD12_TTTCA is on https://stripy.org/database SAMD12_TTTTA is on DRAGON 4.02. The coordinates and pathogenic ranges of the sequence repeats shown above were obtained from DRAGON 4.02 The coordinates https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r4 and https://stripy.org/database were 8:118366815-118366913 (hg38) There is enough evidence for this STR to be green on this panel. This STR has not been approved by NHS STR working group and is not NGS Not Validated Sources: Literature; to: SAMD12 transcribed from the reverse strand, which means that the repeated sequence is the reverse compliment of the forward strand sequence. SAMD12_TTTCA is on https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r3 SAMD12_TTTCA is on https://stripy.org/database SAMD12_TTTTA is on DRAGON 4.02. The coordinates of the sequence repeats shown above were obtained from DRAGON 4.02 The coordinates https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r4 and https://stripy.org/database were 8:118366815-118366913 (hg38) The non-pathogenic and pathogenic ranges of the sequence repeats shown above were obtained from: https://stripy.org/database There is enough evidence for this STR to be green on this panel. This STR has not been approved by NHS STR working group and is not NGS Not Validated Sources: Literature |
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| Early onset or syndromic epilepsy v7.84 | SAMD12_TTTCA | Sarah Leigh commented on STR: SAMD12_TTTCA: The TTTCA repeat is present in conjunction with TTTTA repeats in patients with OMIM:601068. Ishiura et al., 2018 (PMID: 29507423). In patients the expansions TTTCA and TTTTA combined was estimated to be in the range of 440 to 3680 repeats (one patient had 598 repeats of TTTTA and 458 repeats of TTTCA). In 82 patients the configuration of expansion was interpreted as: (TTTTA)exp(TTTCA)exp and in one family it was given as: (TTTTA)exp(TTTCA)exp(TTTTA)exp. There were no reports of TTTCA expansions in controls, however, 5.9% of healthy individuals had TTTTA expansions, therefore suggesting that the TTTTA expansion does no contribute to the disease (Ishiura et al., 2018). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v7.84 | SAMD12_TTTCA | Sarah Leigh Mode of inheritance for STR: SAMD12_TTTCA was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v7.83 | SAMD12_TTTCA | Sarah Leigh Phenotypes for STR: SAMD12_TTTCA were changed from to Epilepsy, familial adult myoclonic, 1, OMIM:601068; epilepsy, familial adult myoclonic, 1, MONDO:0010985 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v7.82 | SAMD12_TTTCA | Sarah Leigh edited their review of STR: SAMD12_TTTCA: Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v7.82 | SAMD12_TTTCA |
Sarah Leigh STR: SAMD12_TTTCA was added STR: SAMD12_TTTCA was added to Early onset or syndromic epilepsy. Sources: Literature STR, NGS Not Validated tags were added to STR: SAMD12_TTTCA. Mode of inheritance for STR: SAMD12_TTTCA was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for STR: SAMD12_TTTCA were set to 30194086; 29507423; 29939203; 32203200 Review for STR: SAMD12_TTTCA was set to AMBER Added comment: SAMD12 transcribed from the reverse strand, which means that the repeated sequence is the reverse compliment of the forward strand sequence. SAMD12_TTTCA is on https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r3 SAMD12_TTTCA is on https://stripy.org/database SAMD12_TTTTA is on DRAGON 4.02. The coordinates and pathogenic ranges of the sequence repeats shown above were obtained from DRAGON 4.02 The coordinates https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r4 and https://stripy.org/database were 8:118366815-118366913 (hg38) There is enough evidence for this STR to be green on this panel. This STR has not been approved by NHS STR working group and is not NGS Not Validated Sources: Literature |
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| Early onset or syndromic epilepsy v4.95 | SAMD12 | Sarah Leigh Publications for gene: SAMD12 were set to 30194086; 29507423; 29939203; 32203200 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.55 | SAMD12 | Sarah Leigh reviewed gene: SAMD12: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.55 | SAMD12 | Sarah Leigh Phenotypes for gene: SAMD12 were changed from Epilepsy, familial adult myoclonic, 1, MIM# 601068 to Epilepsy, familial adult myoclonic, 1, OMIM:601068; epilepsy, familial adult myoclonic, 1, MONDO:0010985 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.54 | SAMD12 | Sarah Leigh Publications for gene: SAMD12 were set to 30194086; 29507423 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.53 | SAMD12 | Sarah Leigh Classified gene: SAMD12 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.53 | SAMD12 | Sarah Leigh Gene: samd12 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.52 | SAMD12 | Sarah Leigh Tag STR tag was added to gene: SAMD12. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v2.40 | SAMD12 |
Zornitza Stark gene: SAMD12 was added gene: SAMD12 was added to Genetic epilepsy syndromes. Sources: Literature Mode of inheritance for gene: SAMD12 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Publications for gene: SAMD12 were set to 30194086; 29507423 Phenotypes for gene: SAMD12 were set to Epilepsy, familial adult myoclonic, 1, MIM# 601068 Mode of pathogenicity for gene: SAMD12 was set to Other Review for gene: SAMD12 was set to GREEN gene: SAMD12 was marked as current diagnostic Added comment: Repeat expansions of intronic TTTCA and TTTTA motifs within SAMD12 have been identified in over 50 Japanese and Chinese families. Most families with affected individuals were heterozygous however 4 patients from 3 families had homozygous repeat expansions, which was associated with a more severe phenotype. Western blot analysis showed decreased levels of the protein in patient brains. Note these were identified on long-read sequencing and may not be detectable by all assays. Sources: Literature |
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