UniProtKB/SwissProt variant VAR

Variant information

Variant position:

398

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 Aspartate (D) to Asparagine (N) at position 398 (D398N, p.Asp398Asn).

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 (D) to medium size and polar (N)

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 CHRNA5 have been associated with susceptibility to smoking-related behavioral traits and lung cancer, contributing to the smoking quantitative trait locus 3 (SQTL3) [MIM:612052].

Additional information on the polymorphism described.

Variant description:

Associated with susceptibility to lung cancer.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs16969968 [ dbSNP | Ensembl ]

Sequence information

Variant position:

398

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

Protein sequence length:

468

The length of the canonical sequence.

Location on the sequence:

EETESGSGPKSSRNTLEAAL D SIRYITRHIMKENDVREVVE

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                         EETESGSGPKSSRNTLEAALDSIRYITRHIMKENDVREVVE

Chimpanzee                    EETESGSGPKSSRNTLEAALDSVRCITRHIMKENDVREVVE

Mouse                         EEAEKDGGPKS-RNTLEAALDCIRYITRHVVKENDVREVVE

Rat                           EEAESGAGPKS-RNTLEAALDCIRYITRHVVKENDVREVVE

Bovine                        EEARSSRGPRSSRNALEAALDSVRYITRHVMKETDVREVVE

Chicken                       EEKGNMSGSESSRNTLEAALDSIRYITRHVMKENEVREVVE

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	23 – 468	Neuronal acetylcholine receptor subunit alpha-5
Topological domain	338 – 429	Cytoplasmic

Literature citations

Comparative structure of human neuronal alpha 2-alpha 7 and beta 2-beta 4 nicotinic acetylcholine receptor subunits and functional expression of the alpha 2, alpha 3, alpha 4, alpha 7, beta 2, and beta 4 subunits.
Elliott K.J.; Ellis S.B.; Berckhan K.J.; Urrutia A.; Chavez-Noriega L.E.; Johnson E.C.; Velicelebi G.; Harpold M.M.;
J. Mol. Neurosci. 7:217-228(1996)
Cited for: NUCLEOTIDE SEQUENCE [MRNA]; VARIANT ASN-398;

Characterization of the genomic structure of human nicotinic acetylcholine receptor CHRNA5/A3/B4 gene cluster: identification of two novel introns in the 3' untranslated region of CHRNA3 and of a tail-to-tail overlap between CHRNA3 and CHRNA5.
Duga S.; Solda G.; Asselta R.; Bonati M.T.; Dalpra L.; Malcovati M.; Tenchini M.L.;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT ASN-398;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P30532: Variant p.Asp398Asn