UniProtKB/SwissProt variant VAR

Variant information

Variant position:

129

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 Methionine (M) to Threonine (T) at position 129 (M129T, p.Met129Thr).

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 (M) 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 rs4242182 [ dbSNP | Ensembl ]

Sequence information

Variant position:

129

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

Protein sequence length:

267

The length of the canonical sequence.

Location on the sequence:

SEDGAAWMQEPGRYSPPPRH M SPTTCTLRKHKTNRKPRTPF

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                         SEDGAAWMQEPGRYSPPPRHMSPTTCTLRKHKTNRKPRTPF

Gorilla                       SEDGAAWMQEPGRYSPPPRHMSPTTCTLRKHKTNRKPRTPF

                              AEDGAAWMQEPGRYSPPPRHMSPTTCTLRKHKTNRKPRTPF

Chimpanzee                    SEDGAAWMQEPGRYSPPPRHMSPTTCTLRKHKTNRKPRXXF

Mouse                         SEDGAPWIQEPGRYSPPPRHMSPTTCTLRKHKTNRKPRTPF

Bovine                        SEDGAAWMQEPGRYSPPPRHMSPTTCTLRKHKTNRKPRTPF

Chicken                       SEDGTSWIQEAGRYSPPPRHLSPTACTLRKHKTNRKPRTPF

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 – 267	Homeobox protein MSX-2
Mutagenesis	147 – 147	T -> A. Does not bind DNA but still suppresses OCFRE activation.

Literature citations

Expression of a human homeobox-containing gene is regulated by 1,25(OH)2D3 in bone cells.
Hodgkinson J.E.; Davidson C.L.; Beresford J.; Sharpe P.T.;
Biochim. Biophys. Acta 1174:11-16(1993)
Cited for: NUCLEOTIDE SEQUENCE [MRNA]; VARIANT THR-129;

A mutation in the homeodomain of the human MSX2 gene in a family affected with autosomal dominant craniosynostosis.
Jabs E.W.; Ma L.; Li X.; Mueller U.; Sparkes R.S.; Luo W.; Jackson C.E.; Warman M.L.; Mulliken J.B.; Snead M.; Haworth I.; Maxson R.E.;
Cell 75:443-450(1993)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT CRS2 HIS-148; VARIANT THR-129;

Molecular cloning and expression of homeobox-containing genes during hard tissue development.
Iimura T.;
Kokubyo Gakkai Zasshi 61:590-604(1994)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA]; VARIANT THR-129;

Cloning of human full-length CDSs in BD Creator(TM) system donor vector.
Kalnine N.; Chen X.; Rolfs A.; Halleck A.; Hines L.; Eisenstein S.; Koundinya M.; Raphael J.; Moreira D.; Kelley T.; LaBaer J.; Lin Y.; Phelan M.; Farmer A.;
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]; VARIANT THR-129;

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 THR-129;

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 THR-129;

Over-expression of HOX-8, the human homologue of the mouse Hox-8 homeobox gene, in human tumors.
Suzuki M.; Tanaka M.; Iwase T.; Naito Y.; Sugimura H.; Kino I.;
Biochem. Biophys. Res. Commun. 194:187-193(1993)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 96-267; VARIANT THR-129;

Functional haploinsufficiency of the human homeobox gene MSX2 causes defects in skull ossification.
Wilkie A.O.M.; Tang Z.; Elanko N.; Walsh S.; Twigg S.R.F.; Hurst J.A.; Wall S.A.; Chrzanowska K.H.; Maxson R.E. Jr.;
Nat. Genet. 24:387-390(2000)
Cited for: VARIANTS PFM1 159-ARG-LYS-160 DEL AND HIS-172; VARIANT THR-129;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P35548: Variant p.Met129Thr