UniProtKB/SwissProt variant VAR

Variant information

Variant position:

60

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 Serine (S) at position 60 (T60S, p.Thr60Ser).

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 polar (S)

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:

Three alleles are known: ADH1B*1 (ADH2*1) corresponding to variant beta-1, ADH1B*2 (ADH2*2) corresponding to variant beta-2, ADH1B*3 (ADH2*3) corresponding to variant beta-3. The sequence shown is that of allele ADH1B*2. The ADH1B*2 allele frequency in orientals is approximately 75%, whereas it is less than 5% in most Caucasian populations. The ADH1B*2 allele is associated with a lower risk of alcoholism. ADH1B variations have been associated with protection against alcohol dependence and alcohol-related aerodigestive tract cancer [MIM:103720].

Additional information on the polymorphism described.

Other resources:

Links to websites of interest for the variant.

Variant rs6413413 [ dbSNP | Ensembl ]

Sequence information

Variant position:

60

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

Protein sequence length:

375

The length of the canonical sequence.

Location on the sequence:

KMVAVGICHTDDHVVSGNLV T PLPVILGHEAAGIVESVGEG

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                         KMVAVGICHTDDHVVSGNLVTPLPVILGHEAAGIVESVGEG

Chimpanzee                    KMVAVGICRTDDHVVSGNLVTPLPAILGHEAAGIVESVGEG

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	2 – 375	All-trans-retinol dehydrogenase [NAD(+)] ADH1B
Metal binding	47 – 47	Zinc 1; catalytic
Metal binding	68 – 68	Zinc 1; catalytic

Literature citations

Submission
NIEHS SNPs program;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS ARG-48; SER-60 AND CYS-370;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P00325: Variant p.Thr60Ser