UniProtKB/SwissProt variant VAR

Variant information

Variant position:

78

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

Type of variant:

Polymorphism

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 Aspartate (D) to Asparagine (N) at position 78 (D78N, p.Asp78Asn).

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 medium size and polar (N)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

1

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:

At least 5 different SAA1 alleles have been described: SAA1.1 (SAA1alpha), SAA1.2 (SAA1beta), SAA1.3 (SAA1gamma), SAA1.4 (SAA1delta), SAA1.5 (also named SAA1beta but which differs from SAA1.2). We use here the revised nomenclature described in PubMed:10211414. The sequence shown is that of SAA1.1.

Additional information on the polymorphism described.

Variant description:

In allele SAA1.4.

Any additional useful information about the variant.

Sequence information

Variant position:

78

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

Protein sequence length:

122

The length of the canonical sequence.

Location on the sequence:

GNYDAAKRGPGGVWAAEAIS D ARENIQRFFGHGAEDSLADQ

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                         GNYDAAKRGPGGVWAAEAISDARENIQRFFGHGAEDSLADQ

Mouse                         GNYDAAQRGPGGVWAAEKISDGREAFQEFFGRGHEDTIADQ

Rabbit                        GNYDAAQRGPGGVWAAKVISDAREDLQRLMGHGAEDSMADQ

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 – 122	Serum amyloid A-1 protein
Chain	19 – 94	Amyloid protein A
Chain	20 – 122	Serum amyloid protein A(2-104)
Chain	20 – 121	Serum amyloid protein A(2-103)
Chain	20 – 120	Serum amyloid protein A(2-102)
Chain	21 – 122	Serum amyloid protein A(3-104)
Chain	22 – 119	Serum amyloid protein A(4-101)
Mutagenesis	65 – 65	R -> A. Reduces affinity for heparin; when associated with A-33 and A-37.
Mutagenesis	80 – 80	R -> A. Reduces affinity for heparin and nearly abolishes association with HDL; when associated with A-18 and A-89.
Mutagenesis	89 – 89	H -> A. Reduces affinity for heparin and nearly abolishes association with HDL; when associated with A-18 and A-80.
Helix	67 – 86

Literature citations

Heterogeneity of human serum amyloid A protein. Five different variants from one individual demonstrated by cDNA sequence analysis.
Steinkasserer A.; Weiss E.H.; Schwaeble W.; Linke R.P.;
Biochem. J. 268:187-193(1990)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 73-122; VARIANTS VAL-75 AND ASN-78;

Identification of two novel amyloid A protein subsets coexisting in an individual patient of AA-amyloidosis.
Baba S.; Takahashi T.; Kasama T.; Shirasawa H.;
Biochim. Biophys. Acta 1180:195-200(1992)
Cited for: PROTEIN SEQUENCE OF 19-94; MASS SPECTROMETRY; DISEASE; VARIANTS ALA-70; VAL-75 AND ASN-78; ALLELE SAA1.3;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P0DJI8: Variant p.Asp78Asn