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HGD mutation databasehomogentisate 1,2-dioxygenase (HGD)
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| Curator: Dr. Andrea Zatkova (andrea.zatkova@savba.sk) | |||
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Coding DNA Reference Sequence: NM_000187.3, the first base of the Met-codon is counted as position 1. Some specific features: Exon: (00) stands for any exon; (i) indicates intron. DNA: (c.?) or wobble code is used when nucleotide change was not known or not indicated Variant original description: brief name of the mutation; if original description of the mutation was different, it is indicated after comma Remarks: description of the variant, AS= acceptor site, DS=donor site Predicted Mutation Effect**: The effects of the novel missense variants on stability and protein-protein afinity was assessed in the context of the molecular interactions of the wild-type residue using mCSM Pires et al. (2014a) and DUET Pires et al. (2014b). Details are downloadable here: TABLE Allele_code: i.e. patient with the Patient_ID (AKU_AQR_11) has alleles AKU_AQR_11a and AKU_AQR_11b Restriction site: mutation abolishes (-) or creates (+) specific restriction site Frequency: of specific polymorphic alleles (AKUdatabase or Vilboux at al. (2009)) Patient_ID: in cases with ID starting with AKU_DB_ we report also HGD haplotypes that can be found in this link: HGD haplotypes associated with AKU mutations DBID: AKU_00000 is used for alleles with unknown mutation References not present in PubMed: Aquaron et al. (2009) (not listed in PubMed): Current Rheumatology Reviews, 2009, 5:111-125. https://doi.org/10.2174/157339709788298419 Cho end Kim (2018) (not listed in PubMed): J Genet Med, 2018, 15:17-19. https://doi.org/10.5734/JGM.2018.15.1.17 Kilavuz et al. (2018) (not listed in PubMed): J. Pediatr. Res. 2018, 5: 7-11. https://doi.org/10.4274/jpr.20982 Akbaba et al. (2020) (not listed in PubMed): JPEM, 33 (2): 289-294, https://doi.org/10.1515/jpem-2019-0163 Mwafi et al. (2021) (not listed in PubMed): AIMS Molecular Science, 8 (1): 60-75, https://doi.org/10.3934/molsci.2021005 Noorian et al. (2018) (not listed in PubMed): Meta Gene, 18: 174-176, https://doi.org/10.1016/j.mgene.2018.09.006 Legend: [ HGD full legend ] Sequence variations are described basically as recommended by the Ad-Hoc Committee for Mutation Nomenclature (AHCMN), with the recently suggested additions (den Dunnen JT and Antonarakis SE [2000], Hum.Mut. 15:7-12); for a summary see Nomenclature. Coding DNA Reference Sequence, with the first base of the Met-codon counted as position 1. Path.: Variant pathogenicity, in the format Reported/Concluded; '+' indicating the variant is pathogenic, '+?' probably pathogenic, '-' no known pathogenicity, '-?' probably no pathogenicity, '?' effect unknown. HGD DB-ID: Database IDentifier; When available, links to OMIM ID's are provided. Exon: Exon numbering. DNA change: Variation at DNA-level. If present, "Full Details" will show you the the full-length entry. RNA change: Variation at RNA-level, (?) unknown but probably identical to DNA. Protein: Variation at protein level. Original description: Variant_original_description Links: Links Variant remarks: Variant remarks Predicted Mutation Effect**: The effects of the novel missense variants on stability and protein-protein afinity was assessed in the context of the molecular interactions of the wild-type residue using mCSM and DUET. Reference: Reference describing the variation, "Submitted:" indicating that the mutation was submitted directly to this database. Mutation HOT-SPOT: mutation_HOT_SPOT Allele code: Allele_code Type: Type of variant at DNA level. Re-site: Variant creates (+) or destroys (-) a restriction enzyme recognition site. Frequency: Frequency if variant is non pathogenic. Template: Variant detected in DNA, RNA and/or Protein. Technique: Technique used to detect the variation. Location: Variant location at DNA level. Patient ID: Internal reference to the patient. Disease: Disease phenotype, as reported in paper/by submitter, unless modified by the curator. Reference: Reference describing the patient, "Submitted:" indicating that the mutation was submitted directly to this database. # Reported: Number of times this case has been reported Geographic origin: Geographic origin of patient Patient/Affected_per_Family: Number of patients per family Families Patients: test |
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