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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37 entries
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AKU_00126 01i c.16-175C>G r.(?) p.(?) ivs1-175C>G rs17140398 polymorphism - Vilboux et al. (2009) - AKU_POL_20 substitution - 0,234(G) DNA SEQ intron
AKU_00107 02i c.87+35A>T r.(?) p.(?) ivs2+35A>T rs2733825 polymorphism - de Bernabe et al. (1998) - AKU_POL_1 substitution - 0,12(T) DNA SEQ intron
AKU_00127 02i c.87+118A>G r.(?) p.(?) ivs2+118A>G rs17140396 polymorphism - Vilboux et al. (2009) - AKU_POL_21 substitution - 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 - - DNA SEQ intron
AKU_00128 03i c.176+114T>A r.(?) p.(?) ivs3+114T>A - polymorphism - Vilboux et al. (2009) - AKU_POL_22 substitution - 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 - 0,45(T) DNA SEQ intron
AKU_00112 03i c.177-52A>C r.(?) p.(?) ivs3-52A>C rs376858353 polymorphism - AKU database - AKU_POL_6 substitution - 0,01(C) DNA SEQ intron
AKU_00111 03i c.177-50C>T r.(?) p.(?) ivs3-50C>T rs145728491 polymorphism - AKU database - AKU_POL_5 substitution - 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 - 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 rs2255543 polymorphism - de Bernabe et al. (1998) - AKU_POL_7 substitution (+)NlaIII 0,22(A) DNA SEQ exon
AKU_00129 04 c.260A>C r.(?) p.(Glu87Ala) E87A rs35702995 missense/polymorphism? Protomer destabilisation, Hexamer disruption Vilboux et al. (2009) - AKU_POL_23 substitution (+)SfaNI - DNA SEQ exon
AKU_00116 04i c.282+31A>G r.(?) p.(?) ivs4+31A>G rs1800722 polymorphism - de Bernabe et al. (1999b) - AKU_POL_10 substitution - 0,02(G) DNA SEQ intron
AKU_00130 04i c.283-145C>T r.(?) p.(?) ivs4-145C>T - polymorphism - Vilboux et al. (2009) - AKU_POL_24 substitution - 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 rs2551607 polymorphism - de Bernabe et al. (1998) - AKU_POL_13 substitution - 0,12(C.) DNA SEQ intron
AKU_00120 06i c.434+46C>A r.(?) p.(?) ivs6+46C>A rs3817627 polymorphism - de Bernabe et al. (1998) - AKU_POL_14 substitution - 0,31(A) DNA SEQ intron
AKU_00131 07i c.469+24C>A r.(?) p.(?) ivs7+24C>A rs756912701 polymorphism - Vilboux et al. (2009) - AKU_POL_25 substitution - 0,013(A) DNA SEQ intron
AKU_00132 08 c.474G>T r.(?) p.(Pro158Pro) P158P rs2293734 polymorphism - Vilboux et al. (2009) CpG AKU_POL_26 substitution (+)EcoNI, DdeI, MnlI; (-)AciI - DNA SEQ exon
AKU_00144 08 c.507T>G r.(?) p.(Phe169Leu) F169L rs756134838 missense Protomer destabilisation Zatkova et al. (2012) - AKU_DB_122b substitution - - DNA SEQ exon
AKU_00106 08i c.549+31C>T r.(?) p.(?) ivs8+31C>T - polymorphism - Vilboux et al. (2009) - AKU_POL_35 substitution - 0,006(T) DNA SEQ intron
AKU_00189 09i c.649+31G>A r.(?) p.(?) ivs9+31G>A rs376223608 polymorphism - Usher et al. (2015) - AKU_DB_122c substitution - - DNA SEQ intron
AKU_00133 09i c.649+104C>T r.(?) p.(?) ivs9+104C>T rs1862942 polymorphism - Vilboux et al. (2009) - AKU_POL_27 substitution - 0,095(T) DNA SEQ intron
AKU_00134 09i c.650-86A>G r.(?) p.(?) ivs9-86A>G rs2075504 polymorphism - Vilboux et al. (2009) - AKU_POL_28 substitution - 0,057(G) DNA SEQ intron
AKU_00067 09i c.650-56G>A
  (Reported 3 times)
r.(spl?) p.(?) ivs9-56G>A - aberrant splicing (AS)/exon skipping - 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 - 0,013(A) DNA SEQ intron
AKU_00068 09i c.650-17G>A r.(spl?) p.(?) ivs9-17G>A - aberrant splicing (AS)/exon skipping - de Bernabe et al. (1998) CCC triplet AKU_DB_10b substitution - - DNA SEQ intron
AKU_00123 11 c.832A>G r.(?) p.(Asn278Asp) N278D rs370920635 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 rs1800700 polymorphism - de Bernabe et al. (1999b) - AKU_POL_16 substitution - 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 - 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 rs112229599 polymorphism, found in one algerian normal chromosome - AKU database - AKU_POL_19 substitution - 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 - 0,025(T) DNA SEQ intron
AKU_00137 13i c.1188+142G>T r.(?) p.(?) ivs13+142G>T rs61799339 polymorphism - Vilboux et al. (2009) - AKU_POL_31 substitution - 0,063(T) DNA SEQ intron
AKU_00138 13i c.1188+203G>A r.(?) p.(?) ivs13+203G>A rs804974 polymorphism - Vilboux et al. (2009) - AKU_POL_32 substitution - 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; (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.
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.