UniProtKB/SwissProt variant VAR

Variant information

Variant position:

350

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

Type of variant:

LP/P [Disclaimer]

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 Phenylalanine (F) to Cysteine (C) at position 350 (F350C, p.Phe350Cys).

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 large size and aromatic (F) to medium size and polar (C)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

-2

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:

In RP35 and CORD10; heterozygous compound with H-345; loss of localization to cell membrane.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs267607034 [ dbSNP | Ensembl ]

Sequence information

Variant position:

350

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

Protein sequence length:

761

The length of the canonical sequence.

Location on the sequence:

VGGTRSSAVCAFSLLDIERV F KGKYKELNKETSRWTTYRGP

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                         VGGTRSSAVCAFSLLDIERVFKGKYKELNKETSRWTTYRGP

Mouse                         VGGTRSSAVCAFSLTDIERVFKGKYKELNKETSRWTTYRGS

Bovine                        VGGTRSSAVCAFSLKDIKSVFEGKYKELDKETSRWTTYEYP

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	33 – 761	Semaphorin-4A
Topological domain	33 – 683	Extracellular
Domain	36 – 494	Sema
Disulfide bond	269 – 379

Literature citations

SEMA4A mutations lead to susceptibility to light irradiation, oxidative stress, and ER stress in retinal pigment epithelial cells.
Tsuruma K.; Nishimura Y.; Kishi S.; Shimazawa M.; Tanaka T.; Hara H.;
Invest. Ophthalmol. Vis. Sci. 53:6729-6737(2012)
Cited for: SUBCELLULAR LOCATION; CHARACTERIZATION OF VARIANT GLN-713; CHARACTERIZATION OF VARIANTS RP35 HIS-345 AND CYS-350;

Identification of novel mutations in the SEMA4A gene associated with retinal degenerative diseases.
Abid A.; Ismail M.; Mehdi S.Q.; Khaliq S.;
J. Med. Genet. 43:378-381(2006)
Cited for: VARIANTS RP35 HIS-345 AND CYS-350; VARIANTS CORD10 HIS-345 AND CYS-350; VARIANT GLN-713;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9H3S1: Variant p.Phe350Cys