View unique variants - HGD mutation database - Leiden Open Variation Database

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The variants below are all in the HGD database. In this view only variant fields are shown. Variants are listed only once, a number is present in the DNA change field when a variant has been reported more than once (in such cases fields other than the DNA change just belong to one entry and may differ for other entries).
Selecting and clicking a specific line will open a detailed view showing all variant entries, including patient and pathogenicity information.
At the bottom of this page a legend is provided with a short explanation of what each field contains.
For a more detailed description of each field, please see the HGD full legend here.

258 entries
entries per page

DB-ID

Exon

DNA change

RNA change

Protein

Original description

Links

Variant remarks

Predicted Mutation Effect**

Reference

Mutation HOT-SPOT

Allele code

Type

Re-site

Frequency

Template

Technique

Location


AKU_00086	12	c.962G>A	r.(?)	p.(Arg321Gln)	R321Q	rs774374625	missense (published nt change is inconsistent with gene sequence, nt change deduced)	Protomer destabilisation	Vilboux et al. (2009)	CpG	AKU_VIL_53b	substitution	(-)TaqI	-	DNA	SEQ	exon
AKU_00087	12	c.964T>C (Reported 2 times)	r.(?)	p.(Trp322Arg)	W322R	-	missense	Hexamer disruption	Rodriguez et al. (2000)	CCC triplet	AKU_DB_48a	substitution	(-)BstXI	-	DNA	SEQ	exon
AKU_00139	12	c.970dupG (Reported 2 times)	r.(?)	p.(Val324Glyfs*3)	V324fs	rs34214309	frameshift	-	Vilboux et al. (2009)	CCC triplet	AKU_POL_33?	insertion	-	-	DNA	SEQ	exon
AKU_00157	12	c.986T>G	r.(?)	p.(Phe329Cys)	F329C	-	missense	Protomer destabilisation	Yang et al. (2013)	-	AKU_DB_163a	substitution	-	-	DNA	SEQ	exon
AKU_00191	12	c.990G>C (Reported 3 times)	r.(?)	p.(Arg330Ser)	R330S	-	missense	Protomer destabilisation	Ascher et al. (2019)	-	AKU_DB_230a	substitution	-	-	DNA	SEQ	exon
AKU_00088	12	c.990G>T (Reported 5 times)	r.(?)	p.(Arg330Ser)	R330S	rs120074171	missense	Protomer destabilisation	de Bernabe et al. (1999b)	-	AKU_DB_37a	substitution	(-)StuI, HaeIII; (+)AhdI	-	DNA	SEQ	exon
AKU_00184	12	c.995C>G (Reported 2 times)	r.(?)	p.(Pro332Arg)	P332R	-	missense	-	Ascher et al. (2019)	-	AKU_TR2_0320b	substitution	?	-	DNA	SEQ	exon
AKU_00089	12i	c.1006+2T>A (Reported 2 times)	r.(spl?)	p.(Asp294Glyfs*4)	ivs12+2T>A	rs1320184173	aberrant splicing (DS)/exon skipping/frameshift?	-	Vilboux et al. (2009)	-	AKU_VIL_70b	substitution	-	-	DNA	SEQ	intron
AKU_00212	12i	c.1006+6T>C	r.(?)	p.(?)	ivs12+6T>C	-	aberrant splicing (DS)/exon skipping/frameshift	-	Cho a Kim 2018	-	AKU_DB_279b	substitution	-	-	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_00090	12i	c.1007-2A>T (Reported 15 times)	r.(spl?)	p.(Arg336Serfs*5)	ivs12-2A>T	rs1261269370	aberrant splicing (AS)/exon skipping/frameshift?	-	Vilboux et al. (2009)	CCC triplet	AKU_VIL_14a	substitution	-	-	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_00196	13	c.1007-1709_1188+1121del (Reported 8 times)	r.(?)	p.(Arg336Serfs*5)	ex13 del	-	deletion	-	Ascher et al. (2019)	-	AKU_DB_11b	deletion	-	-	DNA	SEQ, MLPA	intron/exon
AKU_00236	13	c.1007G>A (Reported 2 times)	r.(?)	p.(Arg336Lys)	R336K	-	missense	Hexamer disruption, Active site disruption	Kilavuz et al. 2018	CCC triplet	AKU_DB_344a	substitution	?	-	DNA	SEQ	exon
AKU_00198	13	c.1007G>C (Reported 2 times)	r.(?)	p.(Arg336Thr)	R336T	-	missense	Hexamer disruption, Active site disruption	Ascher et al. (2019)	CCC triplet	AKU_TR3_0124a	substitution	?	-	DNA	SEQ	exon
AKU_00140	13	c.1008dupG	r.(?)	p.(Asn337Glufs*5)	N337fs	rs35952153	frameshift/splice acceptor site	-	Vilboux et al. (2009)	CCC triplet	AKU_POL_34?	insertion	-	-	DNA	SEQ	exon
AKU_00173	13	c.1009A>G (Reported 2 times)	r.(?)	p.(Asn337Asp)	N337D	-	missense	Protomer destabilisation, Hexamer disruption	Usher et al. (2015)	CCC triplet	AKU_DB_224a	substitution	(+)BsmFI	-	DNA	SEQ	exon
AKU_00091	13	c.1016delT	r.(?)	p.(Met339Argfs*30)	M339fs	-	frameshift	-	Phornphutkul et al. (2002)	-	AKU_PHO_22	substitution	(+)PstI, SfcI	-	DNA	SEQ	exon
AKU_00092	13	c.1017_1019delGAGinsTA (Reported 7 times)	r.(?)	p.(Met339Ilefs*30)	M339fs	rs1057517081	frameshift	-	Vilboux et al. (2009)	-	AKU_VIL_15b	substitution	-	-	DNA	SEQ	exon
AKU_00251	13	c.1019G>T	r.(?)	p.(Ser340Ile)	S340I	-	missense	?	Danda et al. (2020)	-	AKU_DB_381a	substitution	?	-	DNA	SEQ	exon
AKU_00245	13	c.1031delG	r.(?)	p.(Gly344Aspfs*25)	G344fs	rs1295089623	frameshift	-	Lee et al. (2022)	CCC triplet	AKU_DB_423b	deletion	?	-	DNA	SEQ	exon
AKU_00207	13	c.1034T>G (Reported 2 times)	r.(?)	p.(Leu345Arg)	L345R	-	missense	Protomer destabilisation	submitted, Dr. Jeannette Usher	-	AKU_DB_256a	substitution	?	-	DNA	SEQ	exon
AKU_00183	13	c.1037T>C	r.(?)	p.(Ile346Thr)	I346T	rs1299204471	missense	-	Ascher et al. (2019)	-	AKU_TR2_0311a	substitution	?	-	DNA	SEQ	exon
AKU_00252	13	c.1039C>T	r.(?)	p.(Arg347*)	R347*	rs975005146	nonsense	-	Danda et al. (2020)	-	AKU_DB_382a	substitution	?	-	DNA	SEQ	exon
AKU_00199	13	c.1040G>C	r.(?)	p.(Arg347Pro)	R347P	-	missense	Active site disruption	Ascher et al. (2019)	-	AKU_TR3_0125b	substitution	-	-	DNA	SEQ	exon
AKU_00201	13	c.1049A>G	r.(?)	p.(Tyr350Cys)	Y350C	-	missense	-	Ascher et al. (2019)	-	AKU_DB_243b	substitution	?	-	DNA	SEQ	exon
AKU_00154	13	c.1057A>C (Reported 3 times)	r.(?)	p.(Lys353Gln)	K353Q	-	missense	Active site disruption	Nemethova et al. (2016)	-	AKU_DB_31b	substitution	-	-	DNA	SEQ	exon
AKU_00258	13	c.1060C>T (Reported 2 times)	r.(?)	p.(Gln354*)	Q354*	rs780333531	nonsense	-	submitted, Dr. Pelin Teke Kisa	-	AKU_DB_433a	substitution	?	-	DNA	SEQ	exon
AKU_00093	13	c.1075C>T (Reported 2 times)	r.(?)	p.(Pro359Leu)	P359L	rs764037565	missense	Active site disruption	Vilboux et al. (2009)	-	AKU_VIL_5a	substitution	(-)BstNI, ScrFI	-	DNA	SEQ	exon
AKU_00095	13	c.1078G>C (Reported 21 times)	r.(?)	p.(Gly360Arg)	G360R	rs368717991	missense	Protomer destabilisation	Porfirio et al. (2000)	CCC triplet	AKU_DB_30a	substitution	(-)BstNI, ScrFI	-	DNA	SEQ	exon
AKU_00094	13	c.1079G>C (Reported 2 times)	r.(?)	p.(Gly360Ala)	G360A	-	missense	Protomer destabilisation	Zatkova et al. (2012)	CCC triplet	AKU_DB_111a	substitution	(+)FauI; (-)BstNI, ScrFI	-	DNA	SEQ	exon
AKU_00264	13	c.1079G>T (Reported 2 times)	r.(?)	p.(Gly360Val)	G360V	rs1172885188	missense	Protomer destabilisation	Abdelkhalek et al. (2023)	CCC triplet	AKU_DB_442a	substitution	-	-	DNA	SEQ	exon
AKU_00143	13	c.1081G>A (Reported 5 times)	r.(?)	p.(Gly361Arg)	G361R	rs765219004	missense	Protomer destabilisation	Zatkova et al. (2012)	CCC triplet	AKU_DB_121b	substitution	-	-	DNA	SEQ	exon
AKU_00246	13	c.1084G>A	r.(?)	p.(Gly362Arg)	G362R	?	missense	Protomer destabilisation	Lee et al. (2022)	CCC triplet	AKU_DB_424b	substitution	?	-	DNA	SEQ	exon
AKU_00096	13	c.1085G>A (Reported 2 times)	r.(?)	p.(Gly362Glu)	G362E	-	missense	Protomer destabilisation	Phornphutkul et al. (2002)	CCC triplet	AKU_VIL_66a	substitution	(-)MnlI ?	-	DNA	SEQ	exon
AKU_00257	13	c.1095_1100dup	r.(?)	p.(Ser366_Thr367dup)	S366_T367dup	-	insertion inframe	-	Hu et al. (2012)	-	AKU_DB_425b	duplication	?	-	DNA	SEQ	exon
AKU_00097	13	c.1102A>G (Reported 95 times)	r.(?)	p.(Met368Val)	M368V	rs120074173	missense	Hexamer disruption	de Bernabe et al. (1998)	-	AKU_DB_109b	substitution	(+)BtsIMutI, HpyCH4III, Tsp45I, TspRI	-	DNA	SEQ	exon
AKU_00098	13	c.1111dupC (Reported 21 times)	r.(?)	p.(His371Profs*4)	H371fs (P370fs)	rs120074172	frameshift	-	Muller et al. (1999)	CCC triplet	AKU_DB_103b	insertion	(+)BsiYI;BslI	-	DNA	SEQ	exon
AKU_00099	13	c.1112A>G (Reported 3 times)	r.(?)	p.(His371Arg)	H371R	rs120074172	missense	Active site disruption, Hexamer disruption	de Bernabe et al. (1999b)	CCC triplet	AKU_DB_35a	substitution	(-)NcoI	-	DNA	SEQ	exon
AKU_00234	13	c.1114G>A	r.(?)	p.(Gly372Arg)	G372R	rs1940645842	missense	Active site disruption	Soltysova et al. (2021), Bychkov et al. (2021)	-	AKU_DB_335b	substitution	?	-	DNA	SEQ	exon
AKU_00178	13	c.1115_1117del	r.(?)	p.(Gly372_Pro373delinsAla)	G372_P373delinsAla	-	deletion/insertion inframe	-	Ascher et al. (2019)	-	AKU_TR2_0127b	deletion/insertion inframe	?	-	DNA	SEQ	exon
AKU_00178	13	c.1115_1117delGAC	r.(?)	p.(Gly372_Pro373delinsAla)	G372_P373delinsAla	-	deletion/insertion inframe	-	Ascher et al. (2019)	-	AKU_TU_37b	deletion/insertion inframe	?	-	DNA	SEQ	exon
AKU_00100	13	c.1118C>T	r.(?)	p.(Pro373Leu)	P373L	rs138558042	missense	Active site disruption	Vilboux et al. (2009)	-	AKU_VIL_59b	substitution	(-)Sau96I, AvaII	-	DNA	SEQ	exon
AKU_00148	13	c.1120G>C	r.(?)	p.(Asp374His)	D374H	rs981454067	missense	Active site disruption	Zatkova et al. (2012)	-	AKU_DB_125b	substitution	(-)SfaNI	-	DNA	SEQ	exon
AKU_00247	13	c.1157_1160delTGGC	r.(?)	p.(Leu386Hisfs*18)	L386fs	rs772802378	frameshift	-	Lee et al. (2022)	-	AKU_DB_421a	deletion	-	-	DNA	SEQ	exon
AKU_00241	13i	c.1188+1G>A (Reported 2 times)	r.(?)	?	ivs13+1G>A	-	aberrant splicing (DS)/exon skipping/frameshift?	-	Kisa et al. (2021)	-	AKU_TU_15a	substitution	?	-	DNA	SEQ	intron
AKU_00101	13i	c.1188+1G>T (Reported 2 times)	r.(spl?)	p.(Arg336Serfs*5)	ivs13+1G>T	rs760206323	aberrant splicing (DS)/exon skipping/frameshift?	-	Rodriguez et al. (2000)	-	AKU_DB_22b	substitution	-	-	DNA	SEQ	intron
AKU_00228	13i	c.1188+8T>A	r.(?)	p.(?)	ivs13+8T>A	-	aberrant splicing (AS)/exon skipping	-	Soltysova et al. (2021)	-	AKU_DB_314b	substitution	?	-	DNA	SEQ	exon
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
AKU_00204	13i14	c.1189-41_1248del (Reported 6 times)	r.(?)	p.(?)	in13ex14 del	-	deletion	-	Ascher et al. (2019)	-	AKU_DB_239a	deletion	-	-	DNA	SEQ	intron/exon
AKU_00223	14	c.1191A>C	r.(?)	p.(Ala397Ala)	A397A	rs137923025	silent/polymorphism - no effect on splicing	-	Ascher et al. (2019)	-	AKU_DB_287e	substitution	?	-	DNA	SEQ	exon
AKU_00102	14	c.1201G>C (Reported 13 times)	r.(?)	p.(Glu401Gln)	E401Q	rs767159114	missense	Active site disruption, Hexamer disruption	Mannoni et al. (2004)	-	AKU_MAN_2a	substitution	(-)TfiI ?	-	DNA	SEQ	exon
AKU_00103	14	c.1221G>A	r.(spl?)	p.(Ala407Ala)	A407A	rs146206905	silent/aberrant splicing (creating novel DS)	-	Ladjouze-Rezig et al. (2006)	-	AKU_DB_42a	substitution	(-)AciI	-	DNA	SEQ	exon
AKU_00147	14	c.1290_1300del	r.(?)	p.(Lys431Hisfs*11)	K431fs (old description c.1282_1292delGAGCCACTCAA)	rs1553715351	frameshift	-	Zatkova et al. (2012)	-	AKU_DB_124b	deletion	-	-	DNA	SEQ	exon
AKU_00104	14	c.1336T>C (Reported 4 times)	r.(?)	p.(446Argext24)	*446ext	rs143370662	extention	-	Vilboux et al. (2009)	-	AKU_VIL_13b	substitution	(+)Taq1	-	DNA	SEQ	exon

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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.

HGD mutation database

homogentisate 1,2-dioxygenase (HGD)