UniProtKB/Swiss-Prot P12830: Variant p.Thr340Ala

Cadherin-1
Gene: CDH1
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Variant information Variant position:

340 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 Threonine (T) to Alanine (A) at position 340 (T340A, p.Thr340Ala). 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 polar (T) to small size and hydrophobic (A) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score:

0 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:

Found in gastric and colorectal cancer samples; cells exhibited decreased aggregation increased invasiveness and non-uniform migration in vitro compared to cells transfected with wild-type sequence. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs116093741 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

NRNTGVISVVTTGLDRESFP T YTLVVQAADLQGEGLSTTAT 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                         NRNTGVISVVTTGLDRESFPTYTLVVQAADLQ-GEGLSTTAT

                              NKDTGVISVLTTGLDREGVPMYTLVVQAADLQ-GEGLTTTA

Mouse                         NRDTGVISVLTSGLDRESYPTYTLVVQAADLQ-GEGLSTTA

Rat                           NRDTGVISVVTSGLDRESYPTYTLVVQAADLQ-GEGLSTTA

Bovine                        NKETGVISVLTTGLDRESFPTYTLMVQAADLN-GEGLSTTA

Chicken                       DPAKGIISVLGTGLDRETTPNYTLIVQATDQE-GKGLSNTA

Xenopus laevis                HSESGLISVLTTGLDREKNPVYTLTIQAADGEFGKDRTTTA

Zebrafish                     NPVSGGISVLEKGLDREQWFRYTLVITATDMN-GEGLSTTG

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	155 – 882	Cadherin-1
Topological domain	155 – 709	Extracellular
Domain	263 – 375	Cadherin 2
Glycosylation	358 – 358	O-linked (Man...) threonine
Beta strand	340 – 348

Literature citations
The E-cadherin gene (CDH1) variants T340A and L599V in gastric and colorectal cancer patients in Korea.
Kim H.C.; Wheeler J.M.D.; Kim J.C.; Ilyas M.; Beck N.E.; Kim B.S.; Park K.C.; Bodmer W.F.;
Gut 47:262-267(2000)
Cited for: VARIANT ALA-340; Screening E-cadherin in gastric cancer families reveals germline mutations only in hereditary diffuse gastric cancer kindred.
Oliveira C.; Bordin M.C.; Grehan N.; Huntsman D.; Suriano G.; Machado J.C.; Kiviluoto T.; Aaltonen L.; Jackson C.E.; Seruca R.; Caldas C.;
Hum. Mutat. 19:510-517(2002)
Cited for: VARIANT ALA-340; Identification of CDH1 germline missense mutations associated with functional inactivation of the E-cadherin protein in young gastric cancer probands.
Suriano G.; Oliveira C.; Ferreira P.; Machado J.C.; Bordin M.C.; De Wever O.; Bruyneel E.A.; Moguilevsky N.; Grehan N.; Porter T.R.; Richards F.M.; Hruban R.H.; Roviello F.; Huntsman D.; Mareel M.; Carneiro F.; Caldas C.; Seruca R.;
Hum. Mol. Genet. 12:575-582(2003)
Cited for: VARIANTS THR-617 AND VAL-634; CHARACTERIZATION OF VARIANTS ALA-340; THR-617 AND VAL-634;

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.