LOVD - Variant listings for HGD

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+/+ AKU_00017 04 c.179G>A
    + c.179G>A
r.(?) p.(Trp60*) W60* nonsense - Zatkova et al. (2012) - AKU_DB_107a substitution (+)NheI - DNA SEQ exon AKU_DB_107 AKU Zatkova et al. (2012), Slovakia (Slovak Republic):Bratislava Homozygot 1 Italy 1 1
+/+ AKU_00017 04 c.179G>A
    + c.179G>A
r.(?) p.(Trp60*) W60* nonsense - Zatkova et al. (2012) - AKU_DB_107b substitution (+)NheI - DNA SEQ exon AKU_DB_107 AKU Zatkova et al. (2012), Slovakia (Slovak Republic):Bratislava Homozygot 1 Italy 1 1
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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, it is used in case of unknown mutation; (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:
Aquaron et al. (2009) (not listed in PubMed): Aquaron R, Rodriguez de Cordoba S, Penalva M, Badens C, Roux H:
Alkaptonuria, Ochronosis and Ochronotic Arthropathy in Mainland France and the Reunion Island. A Report of Clinical and Molecular Findings.
Current Rheumatology Reviews, 2009, 5:111-125. DOI:10.2174/157339709788298419
Cho end Kim (2018) (not listed in PubMed): Cho, SY and Kim, JH:
Identification of HGD mutations in an alkaptonuria patient:using the internet to seek rare disease. J Genet Med, 2018, 15:17-19.
https://doi.org/10.5734/JGM.2018.15.1.17

WHEN REFERRING TO THE DATABASE, PLEASE CITE:
Zatkova et al. (2012): Zatkova A, Sedlackova T, Radvansky J, Polakova H, Nemethova M, Aquaron R, Dursun I, Usher JL, Kadasi L:
Identification of eleven novel homogentisate 1,2 dioxygenase (HGD) variants in alkaptonuria (AKU) patients and establishment of a novel LOVD based HGD mutation database.
JIMD Reports, 2012, Volume 4, 55-65, DOI: 10.1007/8904_2011_68

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 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