Activity
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| Hereditary ataxia with onset in adulthood v8.12 | PNPT1 |
Lucy Jackson gene: PNPT1 was added gene: PNPT1 was added to Hereditary ataxia with onset in adulthood. Sources: NHS GMS Mode of inheritance for gene: PNPT1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Review for gene: PNPT1 was set to GREEN Added comment: Already green on childhood ataxia panel, see https://panelapp.genomicsengland.co.uk/panels/477/gene/PNPT1/ The ataxia phenotype can manifest in adulthood, therefore suggest adding to this panel also. Sources: NHS GMS |
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| Hereditary ataxia with onset in adulthood v8.12 | ISCA-37404-Loss |
Arina Puzriakova Added comment: Comment on list classification: This region has been deprecated by ClinGen and therefore should be removed from the panel. This region has been subsumed into ISCA-37478 which is green on multiple GMS panels including this panel (https://panelapp.genomicsengland.co.uk/panels/entities/ISCA-37478-Loss) Checked and approved by the Genomics England Clinical team. |
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| Hereditary ataxia with onset in adulthood v7.20 | ATXN8OS_CTG | Sarah Leigh commented on STR: ATXN8OS_CTG: The numbers of ATXN8OS_CTG required for pathogenicity given by https://stripy.org/database are: 2-37 for normal, 38-79 for intermediate and ≥80 for pathogenic and https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r4 gives the repeats as follows: ≤ 50 for normal, 38 - 79 for intermediate and ≥ 71 for pathogenic. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v7.20 | ATXN8OS_CTG |
Sarah Leigh STR: ATXN8OS_CTG was added STR: ATXN8OS_CTG was added to Hereditary ataxia with onset in adulthood. Sources: Literature STR, NGS Not Validated tags were added to STR: ATXN8OS_CTG. Mode of inheritance for STR: ATXN8OS_CTG was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for STR: ATXN8OS_CTG were set to 16804541; 10192387 Phenotypes for STR: ATXN8OS_CTG were set to Spinocerebellar ataxia 8, OMIM:608768; spinocerebellar ataxia type 8, MONDO:0012116 Review for STR: ATXN8OS_CTG was set to GREEN Added comment: ATXN8OS transcribed from the forward strand. ATXN8OS_CTG is on https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r4 ATXN8OS_CTG is on https://stripy.org/database ATXN8OS_CTG is on DRAGON 4.02. The coordinates of the sequence repeats shown above were obtained from DRAGON 4.02, https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r4 and https://stripy.org/database were 4:39348424-39348485 (hg38) The non-pathogenic and pathogenic ranges of the sequence repeats shown above were obtained from: https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r4 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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| Hereditary ataxia with onset in adulthood v7.18 | RFC1_AAGGG |
Sarah Leigh STR: RFC1_AAGGG was added STR: RFC1_AAGGG was added to Hereditary ataxia with onset in adulthood. Sources: Literature STR, NGS Not Validated tags were added to STR: RFC1_AAGGG. Mode of inheritance for STR: RFC1_AAGGG was set to BIALLELIC, autosomal or pseudoautosomal Publications for STR: RFC1_AAGGG were set to 30926972; 35883251; 36250766; 36289003; 36524104; 36478048 Phenotypes for STR: RFC1_AAGGG were set to Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome, OMIM: 614575 Review for STR: RFC1_AAGGG was set to GREEN Added comment: RFC1 transcribed from the reverse strand, which means that the repeated sequence is the reverse compliment of the forward strand sequence. RFC1_AAGGG is on https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r4 RFC1_AAGGG is on https://stripy.org/database RFC1_AARRG is on DRAGON 4.02. The coordinates of the sequence repeats shown above were obtained from DRAGON 4.02 and https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r4 The coordinates of the sequence repeats from https://stripy.org/database were 4:39348424-39348485 (hg38) The non-pathogenic and pathogenic ranges of the sequence repeats shown above were obtained from: https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r4 And 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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| Hereditary ataxia with onset in adulthood v7.17 | DAB1_ATTTC |
Sarah Leigh STR: DAB1_ATTTC was added STR: DAB1_ATTTC was added to Hereditary ataxia with onset in adulthood. Sources: Literature STR, NGS Not Validated tags were added to STR: DAB1_ATTTC. Mode of inheritance for STR: DAB1_ATTTC was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for STR: DAB1_ATTTC were set to 29939198; 28686858 Phenotypes for STR: DAB1_ATTTC were set to Spinocerebellar ataxia 37, OMIM: 615945 Review for STR: DAB1_ATTTC was set to GREEN Added comment: DAB1 is transcribed from the reverse strand, which means that the repeated sequence is the reverse compliment of the forward strand sequence. DAB1_ATTTC is on https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r4 DAB1_ATTTC is on https://stripy.org/database DAB1_ATTTT is on DRAGON 4.02. The coordinates of the sequence repeats shown above were the same on: https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r4 https://stripy.org/database were 8:118366815-118366913 (hg38) and DRAGON 4.02 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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| Hereditary ataxia with onset in adulthood v7.15 | BEAN1_TGGAA |
Sarah Leigh commented on STR: BEAN1_TGGAA: BEAN1 transcribed from the forward strand. BEAN1_TGGAA is on https://gnomad.broadinstitute.org/short-tandem-repeat/SAMD12?dataset=gnomad_r4 BEAN1_TGGAA is on https://stripy.org/database BEAN1_TGGAA is DRAGON 4.02 The coordinates of the sequence repeats shown above were obtained from https://gnomad.broadinstitute.org/short-tandem-repeat/SAMD12?dataset=gnomad_r4 the coordinates were the same on DRAGON 4.02. The coordinates from https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r4 were 16:66490398-66490453 (hg38) The non-pathogenic and pathogenic ranges of the sequence repeats shown above were obtained from: https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r4 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 |
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| Hereditary ataxia with onset in adulthood v7.11 | FGF14_TTC |
Sarah Leigh commented on STR: FGF14_TTC: The name of this STR has been changed from FGF14_GAA to FGF14_TTC as FGF14 is transcribed from the reverse strand of the sequence. The coordinates for the repeated sequence have been updated to those shown in https://stripy.org/database/FGF14. Previously, the coordinates were for the whole gene, rather than the repeated sequence. |
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| Hereditary ataxia with onset in adulthood v2.147 | HTT_CAG | Arina Puzriakova commented on STR: HTT_CAG: STR repeat lengths have been reviewed and confirmed by the NHS Genomic Medicine Service. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v2.145 | HTT_CAG | Arina Puzriakova Normal Number of Repeats for HTT_CAG was changed from 40 to 36. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v2.117 | HTT | Arina Puzriakova Added comment: Comment on mode of inheritance: Lack of phenotypic relevance for SNVs - nucleotide repeat expansion mechanism. Biallelic variants not relevant to this panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v2.117 | HTT | Arina Puzriakova Mode of inheritance for gene: HTT was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to Other | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v2.116 | HTT | Arina Puzriakova Phenotypes for gene: HTT were changed from Huntington disease 143100; Lopes-Maciel-Rodan syndrome, 617432 to Huntington disease, OMIM:143100 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v2.115 | HTT_CAG | Arina Puzriakova Phenotypes for STR: HTT_CAG were changed from Huntington disease 143100 to Huntington disease, OMIM:143100 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v2.25 | HTT_CAG | Arina Puzriakova Tag curated_removed tag was added to STR: HTT_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v2.12 | HTT_CAG | Arina Puzriakova Classified STR: HTT_CAG as No list | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v2.12 | HTT_CAG | Arina Puzriakova Added comment: Comment on list classification: This STR has been removed at the request of GHLs for the GMS Neurology Specialist Test Group as it is available as a core test for R68 Huntington Disease. Inclusion on panels for other neurological CIs raises concerns regarding counselling, and so it has been agreed that HTT_CAG will be excluded from this panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v2.12 | HTT_CAG | Arina Puzriakova Str: htt_cag has been removed from the panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.210 | HTT | Louise Daugherty Classified gene: HTT as Red List (low evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.210 | HTT | Louise Daugherty Added comment: Comment on list classification: As discussed with the GMS Neurology Specialist Test Group webex call 11th September 2019: The Specialist Test Group all agreed that there is only enough evidence to rate this gene Red | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.210 | HTT | Louise Daugherty Gene: htt has been classified as Red List (Low Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.194 | HTT_CAG | Louise Daugherty commented on STR: HTT_CAG: Discussed with the GMS Neurology Specialist Test Group webex call 26th July 2019: The Specialist Test Group all agreed that there is enough evidence to rate this STR Green | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.178 | HTT_CAG | Louise Daugherty Source London North GLH was added to STR: HTT_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.177 | HTT_CAG | Louise Daugherty Source NHS GMS was added to STR: HTT_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.176 | HTT_CAG | Louise Daugherty Source Wessex and West Midlands GLH was added to STR: HTT_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.146 | HTT | Louise Daugherty Phenotypes for gene: HTT were changed from Huntington disease 143100; Huntington disease, 143100, 617432 to Huntington disease 143100; Lopes-Maciel-Rodan syndrome, 617432 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.146 | HTT | Louise Daugherty Phenotypes for gene: HTT were changed from Huntington disease 143100; Huntington disease, 143100, 617432 to Huntington disease 143100; Lopes-Maciel-Rodan syndrome, 617432 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.145 | HTT | Louise Daugherty Mode of inheritance for gene: HTT was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.144 | HTT | Louise Daugherty Classified gene: HTT as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.144 | HTT | Louise Daugherty Gene: htt has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.14 | HTT | Louise Daugherty commented on gene: HTT: Review and rating submitted byJames Polke (North Bristol NHS Trust), on behalf of London North GLH for GMS Neurology specialist test group | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.13 | HTT | Louise Daugherty Source London North GMS was added to HTT. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.11 | HTT | James Polke reviewed gene: HTT: Rating: AMBER; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.9 | HTT | Louise Daugherty Added phenotypes Huntington disease, 143100, 617432 for gene: HTT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.8 | HTT | Louise Daugherty reviewed gene: HTT: Rating: AMBER; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.7 | HTT | Tracy Lester reviewed gene: HTT: Rating: GREEN; Mode of pathogenicity: Other - please provide details in the comments; Publications: ; Phenotypes: Huntington disease, 143100, 617432; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal; Current diagnostic: yes | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.2 | HTT | Louise Daugherty Source NHS GMS was added to HTT. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v1.1 | HTT | Louise Daugherty Source Wessex and West Midlands GLH was added to HTT. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v0.27 | HTT_CAG | Louise Daugherty Classified STR: HTT_CAG as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v0.27 | HTT_CAG | Louise Daugherty Str: htt_cag has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v0.26 | HTT_CAG |
Louise Daugherty STR: HTT_CAG was added STR: HTT_CAG was added to Hereditary ataxia - adult onset. Sources: Expert list STR tags were added to STR: HTT_CAG. Mode of inheritance for STR: HTT_CAG was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Phenotypes for STR: HTT_CAG were set to Huntington disease 143100 Review for STR: HTT_CAG was set to GREEN Added comment: Source PanelApp panels : Hereditary ataxia 1.148 Sources: Expert list |
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| Hereditary ataxia with onset in adulthood v0.5 | HTT |
Eleanor Williams Tag nucleotide-repeat-expansion tag was added to gene: HTT. Tag currently-ngs-unreportable tag was added to gene: HTT. |
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| Hereditary ataxia with onset in adulthood v0.2 | HTT |
Eleanor Williams gene: HTT was added gene: HTT was added to Hereditary ataxia - adult onset. Sources: Brain channelopathy v1.46,Expert Review Red Mode of inheritance for gene: HTT was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Phenotypes for gene: HTT were set to Huntington disease 143100 Mode of pathogenicity for gene: HTT was set to Other - please provide details in the comments |
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