UniProtKB/SwissProt variant VAR

Variant information

Variant position:

88

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

Type of variant:

LP/P [Disclaimer]

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 Methionine (M) to Threonine (T) at position 88 (M88T, p.Met88Thr).

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

Variant description:

In PC2 and SM.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs28928898 [ dbSNP | Ensembl ]

Sequence information

Variant position:

88

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

Protein sequence length:

432

The length of the canonical sequence.

Location on the sequence:

GYGSSFGGVDGLLAGGEKAT M QNLNDRLASYLDKVRALEEA

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                         G----------YGSSFGGVDGLLAGGEKATMQNLNDRLASYLDKVRALEEA

Chimpanzee                    G----------YGSSFGGVDGLLAGGEKATMQNLNDRLASY

Mouse                         G----------YGGNFGGVDGLLAGGEKATMQNLNDRLASY

Rat                           G----------YGGNFGGVDGLLAGGEKATMQNLNDRLASY

Bovine                        GYGSGGYVSGGYGGGFGGVDGLLVGGEKATMQNLNDRLASY

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 – 432	Keratin, type I cytoskeletal 17
Domain	84 – 395	IF rod
Region	84 – 120	Coil 1A
Mutagenesis	103 – 103	R -> A. Down-regulates both proliferation of psoriatic T-cells and IFN-gamma production; suppresses keratinocyte growth when part of the altered peptide epitope S1.
Mutagenesis	106 – 106	E -> A. Down-regulates proliferation of psoriatic T-cells and IFN-gamma production when part of the altered peptide epitope S1.

Literature citations

Mutation report: identification of a germline mutation in keratin 17 in a family with pachyonychia congenita type 2.
Celebi J.T.; Tanzi E.L.; Yao Y.J.; Michael E.J.; Peacocke M.;
J. Invest. Dermatol. 113:848-850(1999)
Cited for: VARIANT PC2 THR-88;

Keratin 17 mutation in pachyonychia congenita type 2 patient with early onset steatocystoma multiplex and Hutchinson-like tooth deformity.
Oh S.-W.; Kim M.Y.; Lee J.S.; Kim S.-C.;
J. Dermatol. 33:161-164(2006)
Cited for: VARIANT PC2 THR-88; VARIANT SM THR-88;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q04695: Variant p.Met88Thr