UniProtKB/SwissProt variant VAR

Variant information

Variant position:

163

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 Glycine (G) to Aspartate (D) at position 163 (G163D, p.Gly163Asp).

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 glycine (G) to medium size and acidic (D)

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 TGCT; a tumor with seminoma and teratoma components; associated with severely impaired but detectable kinase activity; somatic mutation; impairs heterotrimeric complex assembly with STRADA and CAB39; predominantly nuclear localization.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs137853078 [ dbSNP | Ensembl ]

Sequence information

Variant position:

163

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

Protein sequence length:

433

The length of the canonical sequence.

Location on the sequence:

VPEKRFPVCQAHGYFCQLID G LEYLHSQGIVHKDIKPGNLL

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                         VPEKRFPVCQAHGYFCQLIDGLEYLHSQGIVHKDIKPGNLL

Mouse                         VPEKRFPVCQAHGYFRQLIDGLEYLHSQGIVHKDIKPGNLL

Rat                           VPEKRFPVCQAHGYFRQLIDGLEYLHSQGIVHKDIKPGNLL

Chicken                       VPEKRFPVFQAHGYFCQLIDGLEYLHSQGIVHKDIKPGNLL

Xenopus laevis                VQDKHFPVFQAHGYFCQLIDGLEYLHSQGIVHKDIKPGNLL

Slime mold                    APNGRLPPHQSQFIFRQLIEACEYIHSQKILHRDIKPDNIL

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 – 430	Serine/threonine-protein kinase STK11
Domain	49 – 309	Protein kinase
Active site	176 – 176	Proton acceptor
Helix	150 – 169

Literature citations

Structure of the LKB1-STRAD-MO25 complex reveals an allosteric mechanism of kinase activation.
Zeqiraj E.; Filippi B.M.; Deak M.; Alessi D.R.; van Aalten D.M.;
Science 326:1707-1711(2009)
Cited for: X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS) OF 43-347 IN COMPLEX WITH STRADA AND CAB39; ACTIVITY REGULATION; CHARACTERIZATION OF VARIANTS SPORADIC CANCER MET-66; GLY-86; ARG-123; SER-157; ASP-163; PRO-170; SER-171; ARG-174; TYR-176; ASN-177; GLU-181; GLN-199; THR-205; PHE-216; VAL-223; PRO-230; PRO-232; ARG-245; PRO-250; HIS-272; TYR-277; GLN-285 AND SER-315; MUTAGENESIS OF ARG-74; ASP-194 AND PHE-204;

Somatic mutations in LKB1 are rare in sporadic colorectal and testicular tumors.
Avizienyte E.; Roth S.; Loukola A.; Hemminki A.; Lothe R.A.; Stenwig A.E.; Fossaa S.D.; Salovaara R.; Aaltonen L.A.;
Cancer Res. 58:2087-2090(1998)
Cited for: VARIANT TGCT ASP-163;

Mutations and impaired function of LKB1 in familial and non-familial Peutz-Jeghers syndrome and a sporadic testicular cancer.
Ylikorkala A.; Avizienyte E.; Tomlinson I.P.; Tiainen M.; Roth S.; Loukola A.; Hemminki A.; Johansson M.; Sistonen P.; Markie D.; Neale K.; Phillips R.; Zauber P.; Twama T.; Sampson J.; Jaervinen H.; Maekelae T.P.; Aaltonen L.A.;
Hum. Mol. Genet. 8:45-51(1999)
Cited for: CHARACTERIZATION OF VARIANT TGCT ASP-163;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q15831: Variant p.Gly163Asp