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UniProtKB/Swiss-Prot Q8IV08: Variant p.Leu308Pro

Phospholipase D3
Gene: PLD3
Variant information

Variant position:  308
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Unclassified
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants implicated in disease according to literature reports.
  • Polymorphism: Variants not reported to be implicated in disease.
  • Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:  From Leucine (L) to Proline (P) at position 308 (L308P, p.Leu308Pro).
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:  Similar physico-chemical property. Both residues are medium size and hydrophobic.
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

Involvement in disease:  Spinocerebellar ataxia 46 (SCA46) [MIM:617770]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA46 is a slowly progressive, autosomal dominant form with onset in adulthood. {ECO:0000269|PubMed:29053796}. Note=The disease may be caused by mutations affecting the gene represented in this entry.
The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:  In SCA46; unknown pathological significance.
Any additional useful information about the variant.

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

Sequence information

Variant position:  308
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  490
The length of the canonical sequence.

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.







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.

Chain 1 – 490 Phospholipase D3
Topological domain 60 – 490 Lumenal

Literature citations

Rare variants in PLD3 do not affect risk for early-onset Alzheimer disease in a European consortium cohort.
Cacace R.; Van den Bossche T.; Engelborghs S.; Geerts N.; Laureys A.; Dillen L.; Graff C.; Thonberg H.; Chiang H.H.; Pastor P.; Ortega-Cubero S.; Pastor M.A.; Diehl-Schmid J.; Alexopoulos P.; Benussi L.; Ghidoni R.; Binetti G.; Nacmias B.; Sorbi S.; Sanchez-Valle R.; Llado A.; Gelpi E.; Almeida M.R.; Santana I.; Tsolaki M.; Koutroumani M.; Clarimon J.; Lleo A.; Fortea J.; de Mendonca A.; Martins M.; Borroni B.; Padovani A.; Matej R.; Rohan Z.; Vandenbulcke M.; Vandenberghe R.; De Deyn P.P.; Cras P.; van der Zee J.; Sleegers K.; Van Broeckhoven C.;
Hum. Mutat. 36:1226-1235(2015)
Cited for: LACK OF INVOLVEMENT IN ALZHEIMER DISEASE; VARIANTS SER-63; ALA-76; MET-159; CYS-162; SER-173; GLY-175; CYS-188; HIS-222; MET-232; GLN-242; GLY-249; CYS-272; SER-284; VAL-293; LEU-297; TYR-300; PRO-308; ILE-358; ALA-426 AND ARG-429;

Exome sequencing and network analysis identifies shared mechanisms underlying spinocerebellar ataxia.
Nibbeling E.A.R.; Duarri A.; Verschuuren-Bemelmans C.C.; Fokkens M.R.; Karjalainen J.M.; Smeets C.J.L.M.; de Boer-Bergsma J.J.; van der Vries G.; Dooijes D.; Bampi G.B.; van Diemen C.; Brunt E.; Ippel E.; Kremer B.; Vlak M.; Adir N.; Wijmenga C.; van de Warrenburg B.P.C.; Franke L.; Sinke R.J.; Verbeek D.S.;
Brain 140:2860-2878(2017)

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.