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GCH1

From SNPedia
is agene
is mentioned by
Full nameGTP cyclohydrolase 1
Other namesGCH GTPCH
RelatedGCHFR
EntrezGene2643
PheGenI2643
VariationViewer2643
ClinVarGCH1
GeneCardsGCH1
dbSNP2643
DiseasesGCH1
SADR2643
HugeNav2643
wikipediaGCH1
googleGCH1
gopubmedGCH1
EVSGCH1
HEFalMpGCH1
MyGene2GCH1
23andMeGCH1
UniProtP30793
EnsemblENSG00000131979
OMIM600225
# SNPs49
 Max MagnitudeChromosome positionSummary
i5000643
i5000644
i5000649
i5000652
i5000654
i5000655
rs10483639054,839,739
rs1048944334.454,902,402
rs104894434454,844,108
rs104894435454,902,341
rs1048944364.454,845,808
rs1048944374.454,865,379
rs1048944384.454,845,792
rs1048944394.454,902,661
rs1048944404.454,865,349
rs1048944414.454,865,376
rs104894442454,844,023
rs104894443454,844,137
rs1048944444.454,902,522
rs104894445454,845,843
rs1064796560054,902,363
rs1115802654,882,151
rs1214742254,877,297
rs126351018554,902,412
rs137852633454,845,799
rs1712805054,877,161
rs17738966054,835,501
rs200891969054,845,784
rs287817254,906,952
rs375966454,904,861
rs378363754,881,400
rs3783641054,893,421
rs41298442554,844,099
rs4411417054,853,845
rs714251754,840,086
rs752688054,844,851
rs75331284954,902,489
rs77054772254,902,425
rs800401854,883,978
rs800720154,858,130
rs8007267054,912,273
rs841254,843,774
rs886039378054,845,784
rs886039379054,844,138
rs886041708054,902,505
rs96169454654,902,439
rs988395114054,845,787
rs998259054,888,313

GCH1 is the gene responsible for the first, and rate-limiting, step in producing tetrahydrobiopterin (BH4), which is used as a cofactor in the production or conversion of several neurotransmitters.

Please note that reference GCH1 sequences use the reverse strand. Many journal articles will use minus orientation when reporting results, even for cases where the dbSNP orientation is plus. Some of the significant SNPs in this gene have ambiguous flips which can make interpreting things difficult.

GCH1 activity is regulated by GCHFR.

SNPs are common in the GCH1 gene, and most are benign. However, there are both rare and not-so-rare variants that have clinical consequences.

Rare variants associated with dystonia include:


Certain more common variants include:

  • The variants comprising the "X" haplotype
    • The 3 SNPs defining this are: rs8007267(T) - rs3783641(A) - rs10483639(C) (listed in 5' to 3' order based on the GCH1 gene on the reverse strand, and, with alleles as defined in dbSNP on the forward strand)
      • The gs223 genoset defines carriers of a single "X" haplotype, and the gs224 genoset defines 'double cats', i.e. carriers of two X haplotypes (who carry C-A-T alleles for rs10483639-rs3783641-rs8007267)
  • rs841, which is in tight (~85 - 95%) linkage with the X haplotype


And for those wondering which GCH1 gene SNPs in SNPedia are tested by the platforms used by different companies along with ClinVar annotations, here's a table; feel free to suggest more GCH1 SNPs to add to SNPedia if you feel important ones are missing:

 In geneOn microarrayClinVar CLNSIGClinVar CLNDBN
i5000643GCH123andMe v3
23andMe v4
i5000644GCH123andMe v3
23andMe v4
i5000649GCH123andMe v3
23andMe v4
i5000652GCH123andMe v3
23andMe v4
i5000654GCH123andMe v3
23andMe v4
i5000655GCH123andMe v3
23andMe v4
rs10483639GCH123andMe v1
23andMe v2
23andMe v3
Affy GenomeWide 6
23andMe v4
Ancestry v2
rs104894433GCH1Ancestry v25Dystonia 5, Dopa-responsive type
rs104894434GCH1Ancestry v25Dystonia, dopa-responsive, with or without hyperphenylalaninemia, autosomal recessive
rs104894435GCH1Ancestry v25Dystonia, dopa-responsive, with or without hyperphenylalaninemia, autosomal recessive
rs104894436GCH1Ancestry v25Dystonia 5, Dopa-responsive type
rs104894437GCH1Ancestry v25Dystonia 5, Dopa-responsive type
rs104894438GCH1Ancestry v25Dystonia 5, Dopa-responsive type
rs104894439GCH15Dystonia 5, Dopa-responsive type
rs104894440GCH1Ancestry v25Dystonia 5, Dopa-responsive type
rs104894441GCH1Ancestry v25Dystonia 5, Dopa-responsive type
rs104894442GCH1Ancestry v25Dystonia, dopa-responsive, with or without hyperphenylalaninemia, autosomal recessive
rs104894443GCH1Ancestry v25GTP cyclohydrolase I deficiency
rs104894444GCH1Ancestry v25Dystonia 5, Dopa-responsive type
rs104894445GCH1Ancestry v25GTP cyclohydrolase I deficiency
rs1064796560GCH14not provided
rs11158026GCH1Ancestry v2
23andMe v5
rs12147422GCH123andMe v1
23andMe v2
23andMe v3
23andMe v4
rs1263510185GCH1
rs137852633GCH1Ancestry v25Dystonia, dopa-responsive, with or without hyperphenylalaninemia, autosomal recessive
rs17128050GCH1Affy GenomeWide 6
FTDNA2
HumanOmni1Quad
Illumina Human 1M
rs17738966GCH123andMe v1
23andMe v2
23andMe v3
Illumina Human 1M
NatGeo2
23andMe v4
rs200891969GCH1Ancestry v24Dystonia, dopa-responsive
not specified
not provided
rs2878172GCH123andMe v1
23andMe v2
23andMe v3
FTDNA2
FamilyTreeDNA
Illumina Human 1M
23andMe v4
Ancestry v2
rs3759664GCH1Illumina Human 1M
rs3783637GCH123andMe v1
23andMe v2
23andMe v3
FTDNA2
HumanOmni1Quad
Illumina Human 1M
23andMe v4
Ancestry v2
23andMe v5
rs3783641GCH123andMe v1
23andMe v2
23andMe v3
23andMe v4
Ancestry v2
rs41298442GCH123andMe v2
23andMe v3
FTDNA2
FamilyTreeDNA
23andMe v4
Ancestry v2
5Dystonia 5, Dopa-responsive type
Dystonia, dopa-responsive, with or without hyperphenylalaninemia, autosomal recessive
rs4411417GCH123andMe v1
23andMe v2
23andMe v3
23andMe v4
Ancestry v2
rs7142517GCH123andMe v1
23andMe v2
23andMe v3
FTDNA2
FamilyTreeDNA
HumanOmni1Quad
Illumina Human 1M
23andMe v4
Ancestry v2
rs752688GCH123andMe v1
23andMe v2
23andMe v3
FTDNA2
FamilyTreeDNA
23andMe v4
Ancestry v2
rs753312849GCH1
rs770547722GCH1
rs8004018GCH1Ancestry v2
23andMe v3
23andMe v4
FTDNA2
HumanOmni1Quad
Illumina Human 1M
23andMe v5
rs8007201GCH123andMe v1
23andMe v3
Illumina Human 1M
23andMe v4
rs8007267GCH123andMe v1
23andMe v2
23andMe v3
Illumina Human 1M
NatGeo2
23andMe v4
Ancestry v2
rs841GCH123andMe v3
FTDNA2
HumanOmni1Quad
Illumina Human 1M
23andMe v4
2Dystonia, dopa-responsive
GTP cyclohydrolase I deficiency
not specified
rs886039378GCH14not provided
rs886039379GCH15not provided
rs886041708GCH15not provided
rs961694546GCH1
rs988395114GCH14not provided
rs998259GCH123andMe v1
23andMe v2
23andMe v3
Affy GenomeWide 6
FTDNA2
FamilyTreeDNA
23andMe v4