{{Rsnum
|rsid=12960
|Gene=SPG7
|Chromosome=16
|position=89553920
|Orientation=plus
|ReferenceAllele=G
|MissenseAllele=A
|GMAF=0.118
|Assembly=GRCh38
|GenomeBuild=38.1
|dbSNPBuild=141
|geno1=(A;A)
|geno2=(A;G)
|geno3=(G;G)
|Gene_s=SPG7
}}{{ population diversity
| geno1=(A;A)
| geno2=(A;G)
| geno3=(G;G)
| CEU | 1.9 | 25.9 | 72.2
| HCB | 0.0 | 22.2 | 77.8
| JPT | 2.3 | 13.6 | 84.1
| YRI | 0.0 | 0.0 | 100.0
| ASW | 0.0 | 10.7 | 89.3
| CHB | 0.0 | 22.2 | 77.8
| CHD | 0.0 | 0.0 | 0.0
| GIH | 2.1 | 26.8 | 71.1
| LWK | 0.0 | 0.0 | 0.0
| MEX | 0.0 | 23.6 | 76.4
| MKK | 0.0 | 3.3 | 96.7
| TSI | 0.0 | 0.0 | 0.0
| HapMapRevision=28
}}{{Venter SNP
|rsid=12960
|allele=A
|frequency=0.123
|uid=1103645552733
|type=homozygous_SNP
|hugo=SPG7
|ensembl gene=ENSG00000197912
|ensembl transcript=ENST00000268704
|sift=TOLERATED
|disease=Defects in SPG7 are the cause of spastic paraplegia-7 (SPG7) (MIM:607259). SPG7 is a form of autosomal recessive hereditary spastic paraplegia (AR-HSP). HSP is a group of inherited degenerative spinal cord disorders characterized by a slow, gradual, progressive weakness and spasticity (stiffness) of the legs. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. Rate of progression and the severity of symptoms are quite variable.
}}

{{PharmGKB
|RSID=rs12960
|Name_s=SPG7:rs12960 A>G; NM_003119.2:c.2063G>A; NP_003110.1:p.Arg688Gln
|Gene_s=SNORD68, RPL13, SPG7
|Feature=
|Evidence=PubMed ID:20038957
|Annotation=Risk or phenotype-associated allele: G Phenotype: The SPG7:rs12960 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.004 Type of association: CO; TOX
|Drugs=docetaxel; thalidomide
|Drug Classes=
|Diseases=Prostatic Neoplasms
|Curation Level=Curated
|PharmGKB Accession ID=PA165111537
}}

{{GET Evidence
|gene=SPG7
|aa_change=Arg688Gln
|aa_change_short=R688Q
|impact=pharmacogenetic
|qualified_impact=Insufficiently evaluated pharmacogenetic
|inheritance=recessive
|quality_scores=Array
|dbsnp_id=rs12960
|overall_frequency_n=1528
|overall_frequency_d=10756
|overall_frequency=0.14206
|n_genomes=15
|n_genomes_annotated=0
|n_haplomes=16
|n_articles=3
|n_articles_annotated=3
|qualityscore_in_silico=2
|qualitycomment_in_silico=Y
|qualityscore_in_vitro=0
|qualitycomment_in_vitro=Y
|qualityscore_case_control=4
|qualitycomment_case_control=Y
|qualityscore_familial=0
|qualitycomment_familial=Y
|qualityscore_severity=3
|qualitycomment_severity=Y
|qualityscore_treatability=3
|qualitycomment_treatability=Y
|gene_in_genetests=Y
|in_pharmgkb=Y
|pph2_score=0.203
|genetests_testable=Y
|genetests_reviewed=Y
|nblosum100=0
|max_or_disease_name=Spastic Paraplegia 7
|max_or_case_pos=5
|max_or_case_neg=65
|max_or_control_pos=24
|max_or_control_neg=76
|max_or_or=0.244
|autoscore=4
|webscore=N
|n_web_uneval=3
|summary_short=The SPG7 gene (spastic paraplegia 7) encodes the mitochondrial protein paraplegin. Mutations in this gene are associated with hereditary spastic paraplegia (HSP), which is characterized by progressive stiffness and weakness in the lower limbs. The gene is located on Chromosome 16 and consists of 17 exons spanning 52kb. This is the only gene in which mutations are known to cause hereditary spastic paraplegia. Alleles are inherited in an autosomal recessive manner. The R688Q mutation is a single nucleotide polymorphism at exon 15. The polymorphism changes the ancestral allele, G, to an A at base pair 2063. This allele is also known as rs12960, which was shown to be associated with toxicity responses to chemotherapy drugs such as Docetaxel.
}}

{{on chip | 23andMe v3}}
{{on chip | 23andMe v4}}
{{on chip | FTDNA2}}
{{on chip | HumanOmni1Quad}}
{{on chip | Illumina Human 1M}}