UniProtKB/Swiss-Prot O43653: Variant p.Glu30Lys

Prostate stem cell antigen
Gene: PSCA
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Variant information Variant position:

30 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 Glutamate (E) to Lysine (K) at position 30 (E30K, p.Glu30Lys). 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 acidic (E) to large size and basic (K) 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:

Genetic variations in PSCA may influence susceptibility to some cancers. A polymorphism gives rise to an upstream methionine which produces a longer protein of 123 residues associated with various cancers including diffuse-type gastric cancer and urinary bladder cancer. Additional information on the polymorphism described.
Other resources:

Links to websites of interest for the variant.

Variant rs3736001 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

TALLCYSCKAQVSNEDCLQV E NCTQLGEQCWTARIRAVGLL 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                         TALLCYSCKAQVSNEDCLQVENC-TQLGEQCWTARIRAVG-----------------------------LL

Mouse                         AALQCYSCTAQMNNRDCLNVQNC-SLDQHSCFTSRIRAIG-

Slime mold                    DSGSNGNQDIQILINDILN--NCSSSESSSCFGTQWGVVAD

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	12 – 86	Prostate stem cell antigen
Domain	12 – 86	UPAR/Ly6
Glycosylation	31 – 31	N-linked (GlcNAc...) asparagine
Disulfide bond	14 – 39

Literature citations
Genetic variation in PSCA is associated with susceptibility to diffuse-type gastric cancer.
Sakamoto H.; Yoshimura K.; Saeki N.; Katai H.; Shimoda T.; Matsuno Y.; Saito D.; Sugimura H.; Tanioka F.; Kato S.; Matsukura N.; Matsuda N.; Nakamura T.; Hyodo I.; Nishina T.; Yasui W.; Hirose H.; Hayashi M.; Toshiro E.; Ohnami S.; Sekine A.; Sato Y.; Totsuka H.; Ando M.; Takemura R.; Takahashi Y.; Ohdaira M.; Aoki K.; Honmyo I.; Chiku S.; Aoyagi K.; Sasaki H.; Ohnami S.; Yanagihara K.; Yoon K.-A.; Kook M.-C.; Lee Y.-S.; Park S.R.; Kim C.G.; Choi I.J.; Yoshida T.; Nakamura Y.; Hirohashi S.;
Nat. Genet. 40:730-740(2008)
Cited for: FUNCTION; TISSUE SPECIFICITY; INDUCTION; ASSOCIATION WITH SUSCEPTIBILITY TO DIFFUSE-TYPE GASTRIC CANCER; VARIANT LYS-30;

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.