LOVD - Variant listings for HGD

Warning Please note that this overview may not be complete, as variants with unknown effect to the phenotype are left out.

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36 entries
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AKU_00126 01i c.16-175C>G r.(?) p.(?) ivs1-175C>G polymorphism, Rs17140398 - Vilboux et al. (2009) - AKU_POL_20 substitution/polymorphism - 0,234(G) DNA SEQ intron
AKU_00107 02i c.87+35A>T r.(?) p.(?) ivs2+35A>T polymorphism, Rs2733825 - de Bernabe et al. (1998) - AKU_POL_1 substitution/polymorphism - 0,12(T) DNA SEQ intron
AKU_00127 02i c.87+118A>G r.(?) p.(?) ivs2+118A>G polymorphism, Rs17140396 - Vilboux et al. (2009) - AKU_POL_21 substitution/polymorphism - 0,076(G) DNA SEQ intron
AKU_00108 02i c.88-218A>T r.(?) p.(?) ivs2-218A>T polymorphism - Granadino et al. (1997) - AKU_POL_2 substitution/polymorphism - - DNA SEQ intron
AKU_00128 03i c.176+114T>A r.(?) p.(?) ivs3+114T>A polymorphism - Vilboux et al. (2009) - AKU_POL_22 substitution/polymorphism - 0,013(A) DNA SEQ intron
AKU_00109 03i c.177-112C>T r.(?) p.(?) ivs3-112C>T polymorphism - AKU database - AKU_POL_3 substitution/polymorphism - 0,45(T) DNA SEQ intron
AKU_00112 03i c.177-52A>C r.(?) p.(?) ivs3-52A>C polymorphism - AKU database - AKU_POL_6 substitution/polymorphism - 0,01(C) DNA SEQ intron
AKU_00111 03i c.177-50C>T r.(?) p.(?) ivs3-50C>T polymorphism - AKU database - AKU_POL_5 substitution/polymorphism - 0,03(T) DNA SEQ intron
AKU_00110 03i c.177-35T>G r.(?) p.(?) ivs3-35T>G polymorphism - AKU database - AKU_POL_4 substitution/polymorphism - 0,01(G) DNA SEQ intron
AKU_00115 04i al.161-163;(CT)n r.(?) p.(?) HGO-1, D3S4496 polymorphism,GDB:5584234/UniSTS:474553 - Granadino et al. (1997) - AKU_POL_9 dinucleotide repeat - 0,89(al.161);0,11(al.163) DNA SEQ intron
AKU_00114 04i al.175-201;(CA)n r.(?) p.(?) HGO-3, D3S4556 polymorphism - de Bernabe et al. (1998) - AKU_POL_8 dinucleotide repeat - 0,208(al.189);0,2(al.193) DNA SEQ intron
AKU_00113 04 c.240A>T r.(?) p.(His80Gln) H80Q polymorphism, Rs2255543 - de Bernabe et al. (1998) - AKU_POL_7 substitution/polymorphism (+)NlaIII 0,22(A) DNA SEQ exon
AKU_00129 04 c.260A>C r.(?) p.(Glu87Ala) E87A missense/polymorphism?, Rs35702995 Protomer destabilisation, Hexamer disruption Vilboux et al. (2009) - AKU_POL_23 substitution/polymorphism (+)SfaNI - DNA SEQ exon
AKU_00116 04i c.282+31A>G r.(?) p.(?) ivs4+31A>G polymorphism - de Bernabe et al. (1999b) - AKU_POL_10 substitution/polymorphism - 0,02(G) DNA SEQ intron
AKU_00130 04i c.283-145C>T r.(?) p.(?) ivs4-145C>T polymorphism, Rs35702995 - Vilboux et al. (2009) - AKU_POL_24 substitution/polymorphism - 0,032(T) DNA SEQ intron
AKU_00117 04i c.283-14insA r.(?) p.(?) ivs4-14insA polymorphism - AKU database - AKU_POL_11 insertion - 0,01(A) DNA SEQ intron
AKU_00118 04i c.283-4T>C r.(?) p.(?) ivs4-4T>C aberrant splicing (AS)/exon skipping, polymorphism? - AKU database - AKU_POL_12 substitution - 0,001(C) DNA SEQ intron
AKU_00119 05i c.342+25T>C r.(?) p.(?) ivs5+25T>C polymorphism, Rs2551607 - de Bernabe et al. (1998) - AKU_POL_13 substitution/polymorphism - 0,12(C.) DNA SEQ intron
AKU_00120 06i c.434+46C>A r.(?) p.(?) ivs6+46C>A polymorphism, Rs3817627 - de Bernabe et al. (1998) - AKU_POL_14 substitution/polymorphism - 0,31(A) DNA SEQ intron
AKU_00131 07i c.469+24C>A r.(?) p.(?) ivs7+24C>A polymorphism - Vilboux et al. (2009) - AKU_POL_25 substitution/polymorphism - 0,013(A) DNA SEQ intron
AKU_00132 08 c.474G>T r.(?) p.(Pro158Pro) P158P polymorphism, Rs2293734 - Vilboux et al. (2009) CpG AKU_POL_26 substitution/polymorphism (+)EcoNI, DdeI, MnlI; (-)AciI - DNA SEQ exon
AKU_00144 08 c.507T>G r.(?) p.(Phe169Leu) F169L missense Protomer destabilisation Zatkova et al. (2012) - AKU_DB_122b substitution/polymorphism - - DNA SEQ exon
AKU_00106 08i c.549+31C>T r.(?) p.(?) ivs8+31C>T polymorphism - Vilboux et al. (2009) - AKU_POL_35 substitution/polymorphism - 0,006(T) DNA SEQ intron
AKU_00133 09i c.649+104C>T r.(?) p.(?) ivs9+104C>T polymorphism, Rs1862942 - Vilboux et al. (2009) - AKU_POL_27 substitution/polymorphism - 0,095(T) DNA SEQ intron
AKU_00134 09i c.650-86A>G r.(?) p.(?) ivs9-86A>G polymorphism, Rs2075504 - Vilboux et al. (2009) - AKU_POL_28 substitution/polymorphism - 0,057(G) DNA SEQ intron
AKU_00067 09i c.650-56G>A
  (Reported 2 times)
r.(spl?) p.(?) ivs9-56G>A aberrant splicing (AS)/exon skipping, polymorphism? - de Bernabe et al. (1998) CCC triplet AKU_DB_10a substitution - - DNA SEQ intron
AKU_00121 09i c.650-38insA r.(?) p.(?) ivs9-38insA polymorphism - de Bernabe et al. (1998) - AKU_POL_15 substitution/polymorphism - 0,013(A) DNA SEQ intron
AKU_00068 09i c.650-17G>A r.(spl?) p.(?) ivs9-17G>A aberrant splicing (AS)/exon skipping, polymorphism? - de Bernabe et al. (1998) CCC triplet AKU_DB_10b substitution - - DNA SEQ intron
AKU_00123 11 c.832A>G r.(?) p.(Asn278Asp) N278D missense/polymorphism?, found in one normal chromosome Protomer destabilisation AKU database - AKU_POL_17 substitution - - DNA SEQ exon
AKU_00122 11i c.879+18A>G r.(?) p.(?) ivs11+18A>G polymorphism, Rs1800700 - de Bernabe et al. (1999b) - AKU_POL_16 substitution/polymorphism - 0,02(G) DNA SEQ intron
AKU_00135 12i c.1007-170A>G r.(?) p.(?) ivs12-170A>G polymorphism - Vilboux et al. (2009) - AKU_POL_29 substitution/polymorphism - 0,006(G) DNA SEQ intron
AKU_00124 13i al.173-199;(CA)n r.(?) p.(?) HGO-2, D3S4497 polymorphism,GDB:5584249/UniSTS:474554 - Granadino et al. (1997) - AKU_POL_18 dinucleotide repeat - 0,208(al.187) DNA SEQ intron
AKU_00125 13i c.1188+51A>G r.(?) p.(?) ivs13+51A>G polymorphism, found in one algerian normal chromosome - AKU database - AKU_POL_19 substitution/polymorphism - 0,006(G) DNA SEQ intron
AKU_00136 13i c.1188+89C>T r.(?) p.(?) ivs13+89C>T polymorphism - Vilboux et al. (2009) - AKU_POL_30 substitution/polymorphism - 0,025(T) DNA SEQ intron
AKU_00137 13i c.1188+142G>T r.(?) p.(?) ivs13+142G>T polymorphism, Rs61799339 - Vilboux et al. (2009) - AKU_POL_31 substitution/polymorphism - 0,063(T) DNA SEQ intron
AKU_00138 13i c.1188+203G>A r.(?) p.(?) ivs13+203G>A polymorphism, Rs804974 - Vilboux et al. (2009) - AKU_POL_32 substitution/polymorphism - 0,203(T) DNA SEQ intron
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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

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.

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.
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.