UniProtKB/Swiss-Prot O60504: Variant p.Ile556Thr

Vinexin
Gene: SORBS3
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Variant information Variant position:

556 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 Isoleucine (I) to Threonine (T) at position 556 (I556T, p.Ile556Thr). 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 (I) to medium size and polar (T) 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
Other resources:

Links to websites of interest for the variant.

Variant rs2449331 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

AARSARHPSSPSALRSPADP I DLGGQTSPRRTGFSFPTQEP 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                         AARSARHPSSPSALRSPADPIDLGGQTSPRRTGFSFPT--QEP

Mouse                         TAHLSSH-SHPSSI--PVDPTDWGGRTSPRRSAFPFPITLQ

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 – 671	Vinexin
Region	519 – 611	Disordered
Modified residue	544 – 544	Phosphoserine
Modified residue	545 – 545	Phosphoserine
Modified residue	547 – 547	Phosphoserine
Modified residue	551 – 551	Phosphoserine
Modified residue	563 – 563	Phosphoserine

Literature citations
Vinexin: a novel vinculin-binding protein with multiple SH3 domains enhances actin cytoskeletal organization.
Kioka N.; Sakata S.; Kawauchi T.; Amachi T.; Akiyama S.K.; Okazaki K.; Yaen C.; Yamada K.M.; Aota S.;
J. Cell Biol. 144:59-69(1999)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM BETA); ALTERNATIVE SPLICING; MUTAGENESIS; VARIANT THR-556; Submission
Her J.-H.; Gorman D.; Miyajima A.; Bolen J.B.;
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM ALPHA); VARIANT THR-556; DNA sequence and analysis of human chromosome 8.
Nusbaum C.; Mikkelsen T.S.; Zody M.C.; Asakawa S.; Taudien S.; Garber M.; Kodira C.D.; Schueler M.G.; Shimizu A.; Whittaker C.A.; Chang J.L.; Cuomo C.A.; Dewar K.; FitzGerald M.G.; Yang X.; Allen N.R.; Anderson S.; Asakawa T.; Blechschmidt K.; Bloom T.; Borowsky M.L.; Butler J.; Cook A.; Corum B.; DeArellano K.; DeCaprio D.; Dooley K.T.; Dorris L. III; Engels R.; Gloeckner G.; Hafez N.; Hagopian D.S.; Hall J.L.; Ishikawa S.K.; Jaffe D.B.; Kamat A.; Kudoh J.; Lehmann R.; Lokitsang T.; Macdonald P.; Major J.E.; Matthews C.D.; Mauceli E.; Menzel U.; Mihalev A.H.; Minoshima S.; Murayama Y.; Naylor J.W.; Nicol R.; Nguyen C.; O'Leary S.B.; O'Neill K.; Parker S.C.J.; Polley A.; Raymond C.K.; Reichwald K.; Rodriguez J.; Sasaki T.; Schilhabel M.; Siddiqui R.; Smith C.L.; Sneddon T.P.; Talamas J.A.; Tenzin P.; Topham K.; Venkataraman V.; Wen G.; Yamazaki S.; Young S.K.; Zeng Q.; Zimmer A.R.; Rosenthal A.; Birren B.W.; Platzer M.; Shimizu N.; Lander E.S.;
Nature 439:331-335(2006)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]; VARIANT THR-556; 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] (ISOFORMS ALPHA AND BETA); VARIANT THR-556; A quantitative atlas of mitotic phosphorylation.
Dephoure N.; Zhou C.; Villen J.; Beausoleil S.A.; Bakalarski C.E.; Elledge S.J.; Gygi S.P.;
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008)
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-530; SER-551 AND SER-563; VARIANT [LARGE SCALE ANALYSIS] THR-556; IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]; Large-scale proteomics analysis of the human kinome.
Oppermann F.S.; Gnad F.; Olsen J.V.; Hornberger R.; Greff Z.; Keri G.; Mann M.; Daub H.;
Mol. Cell. Proteomics 8:1751-1764(2009)
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2 (ISOFORM BETA); PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-6 (ISOFORM BETA); VARIANT [LARGE SCALE ANALYSIS] THR-556; CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS] (ISOFORM BETA); IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]; Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.
Mayya V.; Lundgren D.H.; Hwang S.-I.; Rezaul K.; Wu L.; Eng J.K.; Rodionov V.; Han D.K.;
Sci. Signal. 2:RA46-RA46(2009)
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-530 AND SER-563; VARIANT [LARGE SCALE ANALYSIS] THR-556; IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]; Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.
Olsen J.V.; Vermeulen M.; Santamaria A.; Kumar C.; Miller M.L.; Jensen L.J.; Gnad F.; Cox J.; Jensen T.S.; Nigg E.A.; Brunak S.; Mann M.;
Sci. Signal. 3:RA3-RA3(2010)
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2 (ISOFORM BETA); PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-395; SER-530; SER-545; SER-551 AND SER-563; PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-6 (ISOFORM BETA); VARIANT [LARGE SCALE ANALYSIS] THR-556; CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS] (ISOFORM BETA); IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]; System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.
Rigbolt K.T.; Prokhorova T.A.; Akimov V.; Henningsen J.; Johansen P.T.; Kratchmarova I.; Kassem M.; Mann M.; Olsen J.V.; Blagoev B.;
Sci. Signal. 4:RS3-RS3(2011)
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-544; SER-545 AND SER-563; VARIANT [LARGE SCALE ANALYSIS] THR-556; IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]; Toward a comprehensive characterization of a human cancer cell phosphoproteome.
Zhou H.; Di Palma S.; Preisinger C.; Peng M.; Polat A.N.; Heck A.J.; Mohammed S.;
J. Proteome Res. 12:260-271(2013)
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-348; SER-395; SER-530; SER-544; SER-545 AND SER-563; VARIANT [LARGE SCALE ANALYSIS] THR-556; IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]; An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.
Bian Y.; Song C.; Cheng K.; Dong M.; Wang F.; Huang J.; Sun D.; Wang L.; Ye M.; Zou H.;
J. Proteomics 96:253-262(2014)
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-348; SER-530; SER-547 AND SER-551; VARIANT [LARGE SCALE ANALYSIS] THR-556; IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]; Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis.
Cantin G.T.; Yi W.; Lu B.; Park S.K.; Xu T.; Lee J.-D.; Yates J.R. III;
J. Proteome Res. 7:1346-1351(2008)
Cited for: VARIANT [LARGE SCALE ANALYSIS] THR-556; IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]; Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.
Daub H.; Olsen J.V.; Bairlein M.; Gnad F.; Oppermann F.S.; Korner R.; Greff Z.; Keri G.; Stemmann O.; Mann M.;
Mol. Cell 31:438-448(2008)
Cited for: VARIANT [LARGE SCALE ANALYSIS] THR-556; IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]; Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.
Gauci S.; Helbig A.O.; Slijper M.; Krijgsveld J.; Heck A.J.; Mohammed S.;
Anal. Chem. 81:4493-4501(2009)
Cited for: VARIANT [LARGE SCALE ANALYSIS] THR-556; IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS];

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