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UniProtKB/Swiss-Prot Q8WXF7: Variant p.Tyr196Cys

Atlastin-1
Gene: ATL1
Variant information

Variant position:  196
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  US
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 Tyrosine (Y) to Cysteine (C) at position 196 (Y196C, p.Tyr196Cys).
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 aromatic (Y) to medium size and polar (C)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -2
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 a patient with hereditary spastic paraplegia; unknown pathological significance; no effect on homodimerization and GTPase activity.
Any additional useful information about the variant.

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



Sequence information

Variant position:  196
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:   YNLSQNVQEDDLQHLQLFTE  Y GRLAMEETFLKPFQSLIFLV
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                         YNLSQNVQEDDLQHLQLFTEYGRLAMEETFLKPFQSLIFLV

Mouse                         YNLSQNVQEDDLQHLQLFTEYGRLAMEETFLKPFQSLIFLV

Rat                           YNLSQNVQEDDLQHLQLFTEYGRLAMEETFLKPFQSLIFLV

Bovine                        YNLSQNVQEDDLQHLQLFTEYGRLAMEETFLKPFQSLIFLV

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 191 – 191 Q -> R. Abolishes homodimerization.
Helix 184 – 199


Literature citations

Structural basis for the nucleotide-dependent dimerization of the large G protein atlastin-1/SPG3A.
Byrnes L.J.; Sondermann H.;
Proc. Natl. Acad. Sci. U.S.A. 108:2216-2221(2011)
Cited for: X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) OF 1-447 IN COMPLEX WITH GDP; FUNCTION; CHARACTERIZATION OF VARIANT CYS-196; CHARACTERIZATION OF VARIANT SPAG3 GLN-217; MUTAGENESIS OF ARG-77; GLN-191 AND HIS-247; SUBUNIT;

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.