UniProtKB/Swiss-Prot O15533: Variant p.Thr260Arg

Tapasin
Gene: TAPBP
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Variant information Variant position:

260 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 Threonine (T) to Arginine (R) at position 260 (T260R, p.Thr260Arg). 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 (T) to large size and basic (R) 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:

The 2 alleles of TAPBP; TAPBP*01 (Tapasin*01) (shown here) and TAPBP*02 (Tapasin*02); are in linkage disequilibria with the HLA-DRB1 locus in a Japanese population. Additional information on the polymorphism described.
Variant description:

In allele TAPBP*01. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs2071888 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

AWDDDEPWGPWTGNGTFWLP T VQPFQEGTYLATIHLPYLQG 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                         AWDDDEPWGPWTGNG----TFWLPTVQPFQEGTYLATIHLPYLQG

                              AWDDDDPWGPWTGNG----TLWLPAVQPFQEGTYLATVHLP

Mouse                         AWDDDEPWGPWTGNG----TFWLPAVKPSQEGVYLATVHLP

Chicken                       --------GTRDGDGVTAVTLRLARPSPGDEGTYICSVFLP

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	21 – 448	Tapasin
Topological domain	21 – 414	Lumenal
Glycosylation	253 – 253	N-linked (GlcNAc...) asparagine
Mutagenesis	253 – 253	N -> Q. Reduces the recruitment of PDIA3 to TAP1-TAP2 transporter.

Literature citations
Cloning and functional characterization of a subunit of the transporter associated with antigen processing.
Li S.; Sjoegren H.-O.; Hellman U.; Pettersson R.F.; Wang P.;
Proc. Natl. Acad. Sci. U.S.A. 94:8708-8713(1997)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); PARTIAL PROTEIN SEQUENCE; VARIANT ARG-260; A critical role for tapasin in the assembly and function of multimeric MHC class I-TAP complexes.
Ortmann B.; Copeman J.; Lehner P.J.; Sadasivan B.; Herberg J.A.; Grandea A.G.; Riddell S.R.; Tampe R.; Spies T.; Trowsdale J.; Cresswell P.;
Science 277:1306-1309(1997)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANT ARG-260; Genomic analysis of the Tapasin gene, located close to the TAP loci in the MHC.
Herberg J.A.; Sgouros J.; Jones T.; Copeman J.; Humphray S.J.; Sheer D.; Cresswell P.; Beck S.; Trowsdale J.;
Eur. J. Immunol. 28:459-467(1998)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT ARG-260; Polymorphism of TAPASIN and its linkage disequilibria with HLA class II genes in the Japanese population.
Furukawa H.; Kashiwase K.; Yabe T.; Ishikawa Y.; Akaza T.; Tadokoro K.; Tohma S.; Inoue T.; Tokunaga K.; Yamamoto K.; Juji T.;
Tissue Antigens 52:279-281(1998)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1); POLYMORPHISM; VARIANT ARG-260; Granulocyte-macrophage colony-stimulating factor modulates tapasin expression in human neutrophils.
El Ouakfaoui S.; Heitz D.; Paquin R.; Beaulieu A.D.;
J. Leukoc. Biol. 65:205-210(1999)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANT ARG-260; Generation of a functional, soluble tapasin protein from an alternatively spliced mRNA.
Gao B.; Williams A.; Sewell A.; Elliott T.;
Genes Immun. 5:101-108(2004)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2); VARIANT ARG-260; Identification of an alternate splice form of tapasin in human melanoma.
Belicha-Villanueva A.; Golding M.; McEvoy S.; Sarvaiya N.; Cresswell P.; Gollnick S.O.; Bangia N.;
Hum. Immunol. 71:1018-1026(2010)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 4); ALTERNATIVE SPLICING; VARIANT ARG-260; The DNA sequence and analysis of human chromosome 6.
Mungall A.J.; Palmer S.A.; Sims S.K.; Edwards C.A.; Ashurst J.L.; Wilming L.; Jones M.C.; Horton R.; Hunt S.E.; Scott C.E.; Gilbert J.G.R.; Clamp M.E.; Bethel G.; Milne S.; Ainscough R.; Almeida J.P.; Ambrose K.D.; Andrews T.D.; Ashwell R.I.S.; Babbage A.K.; Bagguley C.L.; Bailey J.; Banerjee R.; Barker D.J.; Barlow K.F.; Bates K.; Beare D.M.; Beasley H.; Beasley O.; Bird C.P.; Blakey S.E.; Bray-Allen S.; Brook J.; Brown A.J.; Brown J.Y.; Burford D.C.; Burrill W.; Burton J.; Carder C.; Carter N.P.; Chapman J.C.; Clark S.Y.; Clark G.; Clee C.M.; Clegg S.; Cobley V.; Collier R.E.; Collins J.E.; Colman L.K.; Corby N.R.; Coville G.J.; Culley K.M.; Dhami P.; Davies J.; Dunn M.; Earthrowl M.E.; Ellington A.E.; Evans K.A.; Faulkner L.; Francis M.D.; Frankish A.; Frankland J.; French L.; Garner P.; Garnett J.; Ghori M.J.; Gilby L.M.; Gillson C.J.; Glithero R.J.; Grafham D.V.; Grant M.; Gribble S.; Griffiths C.; Griffiths M.N.D.; Hall R.; Halls K.S.; Hammond S.; Harley J.L.; Hart E.A.; Heath P.D.; Heathcott R.; Holmes S.J.; Howden P.J.; Howe K.L.; Howell G.R.; Huckle E.; Humphray S.J.; Humphries M.D.; Hunt A.R.; Johnson C.M.; Joy A.A.; Kay M.; Keenan S.J.; Kimberley A.M.; King A.; Laird G.K.; Langford C.; Lawlor S.; Leongamornlert D.A.; Leversha M.; Lloyd C.R.; Lloyd D.M.; Loveland J.E.; Lovell J.; Martin S.; Mashreghi-Mohammadi M.; Maslen G.L.; Matthews L.; McCann O.T.; McLaren S.J.; McLay K.; McMurray A.; Moore M.J.F.; Mullikin J.C.; Niblett D.; Nickerson T.; Novik K.L.; Oliver K.; Overton-Larty E.K.; Parker A.; Patel R.; Pearce A.V.; Peck A.I.; Phillimore B.J.C.T.; Phillips S.; Plumb R.W.; Porter K.M.; Ramsey Y.; Ranby S.A.; Rice C.M.; Ross M.T.; Searle S.M.; Sehra H.K.; Sheridan E.; Skuce C.D.; Smith S.; Smith M.; Spraggon L.; Squares S.L.; Steward C.A.; Sycamore N.; Tamlyn-Hall G.; Tester J.; Theaker A.J.; Thomas D.W.; Thorpe A.; Tracey A.; Tromans A.; Tubby B.; Wall M.; Wallis J.M.; West A.P.; White S.S.; Whitehead S.L.; Whittaker H.; Wild A.; Willey D.J.; Wilmer T.E.; Wood J.M.; Wray P.W.; Wyatt J.C.; Young L.; Younger R.M.; Bentley D.R.; Coulson A.; Durbin R.M.; Hubbard T.; Sulston J.E.; Dunham I.; Rogers J.; Beck S.;
Nature 425:805-811(2003)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]; VARIANT ARG-260; 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 ARG-260; 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] (ISOFORM 3); VARIANT ARG-260;

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.