LOVD - Variant listings for HGD

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DB-ID Hide DB-ID column Descending
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Exon Hide Exon column Descending
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RNA change Hide RNA change column Descending
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Original description Hide Original description column Descending
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Variant remarks Hide Variant remarks column Descending
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Predicted Mutation Effect** Hide Predicted Mutation Effect** column Descending
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Reference Hide Reference column Descending
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Allele code Hide Allele code column Descending
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+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_8a substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_8 AKU de Bernabe et al. (1998), Slovakia (Slovak Republic):Bratislava Homozygot 1 United Kingdom 1 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_8b substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_8 AKU de Bernabe et al. (1998), Slovakia (Slovak Republic):Bratislava Homozygot 1 United Kingdom 1 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_VIL_22a substitution (+)HhaI, FspI - DNA SEQ exon AKU_VIL_22 AKU Vilboux et al. (2009), Slovakia (Slovak Republic):Bratislava Homozygot 1 USA 1 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_VIL_22b substitution (+)HhaI, FspI - DNA SEQ exon AKU_VIL_22 AKU Vilboux et al. (2009), Slovakia (Slovak Republic):Bratislava Homozygot 1 USA 1 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_VIL_34a substitution (+)HhaI, FspI - DNA SEQ exon AKU_VIL_34 AKU Vilboux et al. (2009), Slovakia (Slovak Republic):Bratislava Homozygot 1 USA 1 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_VIL_34b substitution (+)HhaI, FspI - DNA SEQ exon AKU_VIL_34 AKU Vilboux et al. (2009), Slovakia (Slovak Republic):Bratislava Homozygot 1 USA 1 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_VIL_9a substitution (+)HhaI, FspI - DNA SEQ exon AKU_VIL_9 AKU Vilboux et al. (2009), Slovakia (Slovak Republic):Bratislava Homozygot 1 USA 1 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_VIL_9b substitution (+)HhaI, FspI - DNA SEQ exon AKU_VIL_9 AKU Vilboux et al. (2009), Slovakia (Slovak Republic):Bratislava Homozygot 1 USA 1 1
+/+ AKU_00008 03 c.125A>C
    + c.1102A>G
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_133a substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_133 AKU Zatkova et al. (2012), United Kingdom (Great Britain):Liverpool Compound heterozygous 1 United Kingdom 2 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_134a substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_134 AKU Zatkova et al. (2012); Usher et al. (2015), United Kingdom (Great Britain):Liverpool Homozygot 1 United Kingdom 2 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_134b substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_134 AKU Zatkova et al. (2012); Usher et al. (2015), United Kingdom (Great Britain):Liverpool Homozygot 1 United Kingdom 2 1
+/+ AKU_00008 03 c.125A>C
    + c.359G>T
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_203b substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_203 AKU Usher et al. (2015), United Kingdom (Great Britain):Liverpool Compound heterozygous 1 United Kingdom 1 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_204a substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_204 AKU Usher et al. (2015), United Kingdom (Great Britain):Liverpool Homozygot 1 United Kingdom 2 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_204b substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_204 AKU Usher et al. (2015), United Kingdom (Great Britain):Liverpool Homozygot 1 United Kingdom 2 1
+/+ AKU_00008 03 c.125A>C
    + c.481G>A
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_221a substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_221 AKU Usher et al. (2015), United Kingdom (Great Britain):Liverpool Compound heterozygous 1 United Kingdom 1 1
+/+ AKU_00008 03 c.125A>C
    + c.(?)
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_223b substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_223 AKU Usher et al. (2015), United Kingdom (Great Britain):Liverpool Compound heterozygous 1 United Kingdom 1 1
+/+ AKU_00008 03 c.125A>C
    + c.899T>G
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_225a substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_225 AKU Usher et al. (2015), United Kingdom (Great Britain):Liverpool Compound heterozygous 1 United Kingdom 1 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_255a substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_255 AKU submitted, United Kingdom (Great Britain):Liverpool Homozygot 1 United Kingdom 2 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_255b substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_255 AKU submitted, United Kingdom (Great Britain):Liverpool Homozygot 1 United Kingdom 2 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_259a substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_259 AKU submitted, United Kingdom (Great Britain):Liverpool Homozygot 1 United Kingdom 1 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_259b substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_259 AKU submitted, United Kingdom (Great Britain):Liverpool Homozygot 1 United Kingdom 1 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_260a substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_260 AKU submitted, United Kingdom (Great Britain):Liverpool Homozygot 1 United Kingdom 1 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_260b substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_260 AKU submitted, United Kingdom (Great Britain):Liverpool Homozygot 1 United Kingdom 1 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_261a substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_261 AKU submitted, United Kingdom (Great Britain):Liverpool Homozygot 1 United Kingdom 1 1
+/+ AKU_00008 03 c.125A>C
    + c.125A>C
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_261b substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_261 AKU submitted, United Kingdom (Great Britain):Liverpool Homozygot 1 United Kingdom 1 1
+/+ AKU_00008 03 c.125A>C
    + c.457G>A
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_253b substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_253 AKU submitted, United Kingdom (Great Britain):Liverpool Compound heterozygous 1 United Kingdom 1 1
+/+ AKU_00008 03 c.125A>C
    + c.1102A>G
r.(?) p.(Glu42Ala) E42A missense Protomer destabilisation, Hexamer disruption de Bernabe et al. (1998) - AKU_DB_263b substitution (+)HhaI, FspI - DNA SEQ exon AKU_DB_263 AKU submitted, United Kingdom (Great Britain):Liverpool Compound heterozygous 1 United Kingdom 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