Home  |  Contact

UniProtKB/Swiss-Prot Q8WXF7: Variant p.Arg239Cys

Atlastin-1
Gene: ATL1
Variant information

Variant position:  239
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  LP/P [Disclaimer]
The variants are classified into three categories: LP/P, LB/B and US.
  • LP/P: likely pathogenic or pathogenic.
  • LB/B: likely benign or benign.
  • US: uncertain significance

Residue change:  From Arginine (R) to Cysteine (C) at position 239 (R239C, p.Arg239Cys).
Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.

Physico-chemical properties:  Change from large size and basic (R) to medium size and polar (C)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -3
The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:
  • Lowest score: -4 (low probability of substitution).
  • Highest score: 11 (high probability of substitution).
More information can be found on the following page

Variant description:  In SPG3; affects endoplasmic reticulum and Golgi morphology.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  239
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  558
The length of the canonical sequence.

Location on the sequence:   WSFPYEFSYGADGGAKFLEK  R LKVSGNQHEELQNVRKHIHS
The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.

Residue conservation: 
The multiple alignment of the region surrounding the variant against various orthologous sequences.

Human                         WSFPYEFSYGADGGAKFLEKRLKVSGNQHEELQNVRKHIHS

Mouse                         WSFPYEFSYGADGGAKFLEKRLKVSGNQHEELQNVRKHIHS

Rat                           WSFPYEFSYGADGGAKFLEKRLKVSGNQHEELQNVRKHIHS

Bovine                        WSFPYEFSYGSDGGSKFLEKRLKVSGNQHEELQNVRKHIHS

Sequence annotation in neighborhood:  
The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:
  • Type: the type of sequence feature.
  • Positions: endpoints of the sequence feature.
  • Description: contains additional information about the feature.

TypePositionsDescription
Chain 1 – 558 Atlastin-1
Topological domain 1 – 449 Cytoplasmic
Domain 64 – 309 GB1/RHD3-type G
Mutagenesis 247 – 247 H -> R. Impairs homodimerization and GTPase activity.
Helix 229 – 240


Literature citations

Mutations in a newly identified GTPase gene cause autosomal dominant hereditary spastic paraplegia.
Zhao X.; Alvarado D.; Rainier S.; Lemons R.; Hedera P.; Weber C.H.; Tukel T.; Apak M.; Heiman-Patterson T.; Ming L.; Bui M.; Fink J.K.;
Nat. Genet. 29:326-331(2001)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANTS SPG3 CYS-239; ARG-258 AND TYR-259;

Mutations in the SPG3A gene encoding the GTPase atlastin interfere with vesicle trafficking in the ER/Golgi interface and Golgi morphogenesis.
Namekawa M.; Muriel M.-P.; Janer A.; Latouche M.; Dauphin A.; Debeir T.; Martin E.; Duyckaerts C.; Prigent A.; Depienne C.; Sittler A.; Brice A.; Ruberg M.;
Mol. Cell. Neurosci. 35:1-13(2007)
Cited for: FUNCTION; SUBCELLULAR LOCATION; CHARACTERIZATION OF VARIANTS SPG3 PRO-161; CYS-239 AND TRP-495; MUTAGENESIS OF PHE-151; THR-162 AND SER-398; INTERACTION WITH TMED2; TISSUE SPECIFICITY;

Mutational spectrum of the SPG4 (SPAST) and SPG3A (ATL1) genes in Spanish patients with hereditary spastic paraplegia.
Alvarez V.; Sanchez-Ferrero E.; Beetz C.; Diaz M.; Alonso B.; Corao A.I.; Gamez J.; Esteban J.; Gonzalo J.F.; Pascual-Pascual S.I.; Lopez de Munain A.; Moris G.; Ribacoba R.; Marquez C.; Rosell J.; Marin R.; Garcia-Barcina M.J.; Del Castillo E.; Benito C.; Coto E.;
BMC Neurol. 10:89-89(2010)
Cited for: VARIANTS SPG3 GLU-154; CYS-239; ILE-253; VAL-413; TRP-415; THR-440 AND TRP-495;

Mutation screening of spastin, atlastin, and REEP1 in hereditary spastic paraplegia.
McCorquodale D.S. III; Ozomaro U.; Huang J.; Montenegro G.; Kushman A.; Citrigno L.; Price J.; Speziani F.; Pericak-Vance M.A.; Zuchner S.;
Clin. Genet. 79:523-530(2011)
Cited for: VARIANT CYS-196; VARIANTS SPG3 CYS-239; ILE-253 AND TRP-495;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.