UniProtKB/Swiss-Prot O95477: Variant p.Val399Ala

Phospholipid-transporting ATPase ABCA1
Gene: ABCA1
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Variant information Variant position:

399 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 Valine (V) to Alanine (A) at position 399 (V399A, p.Val399Ala). 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 hydrophobic (V) to small size and hydrophobic (A) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score:

0 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 ABCA1 define the high density lipoprotein cholesterol level quantitative trait locus 13 (HDLCQ13) [MIM:600046]. Additional information on the polymorphism described.
Other resources:

Links to websites of interest for the variant.

Variant rs9282543 [ dbSNP | Ensembl ]

Sequence information Variant position:

399 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

2261 The length of the canonical sequence.
Location on the sequence:

LVGKILYTPDTPATRQVMAE V NKTFQELAVFHDLEGMWEEL 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                         LVGKILYTPDTPATRQVMAEVNKTFQELAVFHDLEGMWEEL

Mouse                         LVGKILYTPDTPATRQVMAEVNKTFQELAVFHDLEGMWEEL

Slime mold                    LKGGLI----------MMNSIEDSF-EFVLAH---------

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	1 – 2261	Phospholipid-transporting ATPase ABCA1
Topological domain	43 – 639	Extracellular
Glycosylation	400 – 400	N-linked (GlcNAc...) asparagine
Helix	390 – 404

Literature citations
The gene encoding ATP-binding cassette transporter 1 is mutated in Tangier disease.
Bodzioch M.; Orso E.; Klucken J.; Langmann T.; Boettcher A.; Diederich W.; Drobnik W.; Barlage S.; Buechler C.; Porsch-Oezcueruemez M.; Kaminski W.E.; Hahmann H.W.; Oette K.; Rothe G.; Aslanidis C.; Lackner K.J.; Schmitz G.;
Nat. Genet. 22:347-351(1999)
Cited for: VARIANTS TGD SER-590; SER-935 AND VAL-937; VARIANTS ALA-399 AND MET-883; Common genetic variation in ABCA1 is associated with altered lipoprotein levels and a modified risk for coronary artery disease.
Clee S.M.; Zwinderman A.H.; Engert J.C.; Zwarts K.Y.; Molhuizen H.O.F.; Roomp K.; Jukema J.W.; van Wijland M.; van Dam M.; Hudson T.J.; Brooks-Wilson A.; Genest J. Jr.; Kastelein J.J.P.; Hayden M.R.;
Circulation 103:1198-1205(2001)
Cited for: VARIANTS LYS-219; ALA-399; MET-771; PRO-774; ASN-776; ILE-825; MET-883; ASP-1172; ARG-1587 AND CYS-1731;

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.