UniProtKB/SwissProt variant VAR

Variant information

Variant position:

409

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

Type of variant:

LB/B

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 Aspartate (D) to Alanine (A) at position 409 (D409A, p.Asp409Ala).

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 medium size and acidic (D) to small size and hydrophobic (A)

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

Polymorphism:

Genetic variations in LIPC define the high density lipoprotein cholesterol level quantitative trait locus 12 (HDLCQ12) [MIM:612797].Genetic variations in LIPC are associated with non-insulin-dependent diabetes mellitus susceptibility (NIDDM susceptibility) [MIM:125853]. -

Additional information on the polymorphism described.

Other resources:

Links to websites of interest for the variant.

Variant rs142036980 [ dbSNP | Ensembl ]

Sequence information

Variant position:

409

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

Protein sequence length:

499

The length of the canonical sequence.

Location on the sequence:

TLGKGIASNKTYSFLITLDV D IGELIMIKFKWENSAVWANV

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                         TLGKGIASNKTYSFLITLDVDIGELIMIKFKWENSAVWANV

Mouse                         TLGEGITSNKTYSFLITLDKDIGELILLKFKWENSAVWANV

Rat                           TLGEGITSNKTYSLLITLNKDIGELIMLKFKWENSAVWANV

Bovine                        TLSKGITSNETYSFLITLDVDIGELIMIKFKWENRMVWSNV

Rabbit                        TLGEGITSNKTYSFLITLNLDIGELMVIKFKWENSAVWANV

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.

Type	Positions	Description
Chain	23 – 499	Hepatic triacylglycerol lipase
Domain	352 – 486	PLAT
Glycosylation	397 – 397	N-linked (GlcNAc...) asparagine

Literature citations

Association of extreme blood lipid profile phenotypic variation with 11 reverse cholesterol transport genes and 10 non-genetic cardiovascular disease risk factors.
Morabia A.; Cayanis E.; Costanza M.C.; Ross B.M.; Flaherty M.S.; Alvin G.B.; Das K.; Gilliam T.C.;
Hum. Mol. Genet. 12:2733-2743(2003)
Cited for: VARIANTS MET-95; SER-215; PHE-289; ILE-342; LEU-356; MET-405 AND ALA-409;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P11150: Variant p.Asp409Ala