UniProtKB/SwissProt variant VAR

Variant information

Variant position:

115

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 Serine (S) to Threonine (T) at position 115 (S115T, p.Ser115Thr).

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 small size and polar (S) to medium size and polar (T)

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 SEMA7A define the John Milton Hagen blood group system (JMH) [MIM:614745]. Three different JMH phenotypes have been identified based on the presence or absence of the high-frequency JMH antigen: JMH-weak, JMH-negative, and JMH-variant. The JMH-weak and -negative phenotypes can be either acquired or inherited and are characterized by a reduction or complete loss of JMH expression on red blood cells. Individuals with the JMH-variant phenotype are usually JMH-positive and have alloantibodies compatible with JMH-negative red blood cells. The JMH-variant phenotype results from rare SEMA7A missense variants.

Additional information on the polymorphism described.

Other resources:

Links to websites of interest for the variant.

Variant rs16968733 [ dbSNP | Ensembl ]

Sequence information

Variant position:

115

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

Protein sequence length:

666

The length of the canonical sequence.

Location on the sequence:

VYLFDFPEGKNASVRTVNIG S TKGSCLDKRDCENYITLLER

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                         VYLFDFPEGKNASVRTVNIGSTKGSCLDKRDCENYITLLER

Mouse                         VYHFNFPEGKNASVRTVNIGSTKGSCQDKQDCGNYITLLER

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	45 – 648	Semaphorin-7A
Domain	53 – 490	Sema
Modified residue	135 – 135	Asymmetric dimethylarginine
Glycosylation	105 – 105	N-linked (GlcNAc...) asparagine
Alternative sequence	111 – 124	Missing. In isoform 2.

Literature citations

Submission
SeattleSNPs variation discovery resource;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT THR-115;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O75326: Variant p.Ser115Thr