UniProtKB/Swiss-Prot P35542: Variant p.Cys89Tyr

Serum amyloid A-4 protein
Gene: SAA4
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Variant information Variant position:

89 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 Cysteine (C) to Tyrosine (Y) at position 89 (C89Y, p.Cys89Tyr). 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 polar (C) to large size and aromatic (Y) 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:

Confirmed at protein level. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs2460827 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

GVWAAKLISRSRVYLQGLID C YLFGNSSTVLEDSKSNEKAE 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                         GVWAAKLISRSRVYLQGLIDCYLFGNSSTVLEDSKSNEKAE

Mouse                         GIWAAKIISTSRKYFQGLLNRYYFGIRNHGLETLQATQKAE

Pig                           GIWAAKIISNVGEYFQGLLQ--YLGSSSEREEDQVSNRRAE

Bovine                        GVWAAKIISNVGEYLQGFLYQIYLGD-SYGLEDQVSNRRAE

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	19 – 130	Serum amyloid A-4 protein
Glycosylation	94 – 94	N-linked (GlcNAc...) asparagine; partial

Literature citations
Identification of novel members of the serum amyloid A protein superfamily as constitutive apolipoproteins of high density lipoprotein.
Whitehead A.S.; Debeer M.C.; Steel D.M.; Rits M.; Lelias J.M.; Lane W.S.; Debeer F.C.;
J. Biol. Chem. 267:3862-3867(1992)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT TYR-89; A constitutively expressed serum amyloid A protein gene (SAA4) is closely linked to, and shares structural similarities with, an acute-phase serum amyloid A protein gene (SAA2).
Steel D.M.; Sellar G.C.; Uhlar C.M.; Simon S.; Debeer F.C.; Whitehead A.S.;
Genomics 16:447-454(1993)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT TYR-89; Analysis of the genomic and derived protein structure of a novel human serum amyloid A gene, SAA4.
Watson G.; Coade S.; Woo P.;
Scand. J. Immunol. 36:703-712(1992)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT TYR-89; Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201).
Ebert L.; Schick M.; Neubert P.; Schatten R.; Henze S.; Korn B.;
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]; VARIANT TYR-89; Submission
Mural R.J.; Istrail S.; Sutton G.G.; Florea L.; Halpern A.L.; Mobarry C.M.; Lippert R.; Walenz B.; Shatkay H.; Dew I.; Miller J.R.; Flanigan M.J.; Edwards N.J.; Bolanos R.; Fasulo D.; Halldorsson B.V.; Hannenhalli S.; Turner R.; Yooseph S.; Lu F.; Nusskern D.R.; Shue B.C.; Zheng X.H.; Zhong F.; Delcher A.L.; Huson D.H.; Kravitz S.A.; Mouchard L.; Reinert K.; Remington K.A.; Clark A.G.; Waterman M.S.; Eichler E.E.; Adams M.D.; Hunkapiller M.W.; Myers E.W.; Venter J.C.;
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]; VARIANT TYR-89; The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
The MGC Project Team;
Genome Res. 14:2121-2127(2004)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]; VARIANT TYR-89; Quantitative detection of single amino acid polymorphisms by targeted proteomics.
Su Z.D.; Sun L.; Yu D.X.; Li R.X.; Li H.X.; Yu Z.J.; Sheng Q.H.; Lin X.; Zeng R.; Wu J.R.;
J. Mol. Cell Biol. 3:309-315(2011)
Cited for: VARIANT TYR-89; IDENTIFICATION BY MASS SPECTROMETRY;

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.