UniProtKB/SwissProt variant VAR

Variant information

Variant position:

296

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

Type of variant:

Disease [Disclaimer]

The variants are classified into three categories: Disease, Polymorphism and Unclassified.

Disease: Variants implicated in disease according to literature reports.
Polymorphism: Variants not reported to be implicated in disease.
Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:

From Arginine (R) to Cysteine (C) at position 296 (R296C, p.Arg296Cys).

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 basic (R) to medium size and polar (C)

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

BLOSUM score:

-3

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

Involvement in disease:

Non-ketotic hyperglycinemia (NKH) [MIM:605899]: Autosomal recessive disease characterized by accumulation of a large amount of glycine in body fluid and by severe neurological symptoms. {ECO:0000269|PubMed:10873393, ECO:0000269|PubMed:11286506, ECO:0000269|PubMed:16051266, ECO:0000269|PubMed:26371980, ECO:0000269|PubMed:28244183, ECO:0000269|PubMed:8005589, ECO:0000269|PubMed:9600239, ECO:0000269|PubMed:9621520}. Note=The disease is caused by mutations affecting the gene represented in this entry.

The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:

In NKH.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs1056820947 [ dbSNP | Ensembl ]

Sequence information

Variant position:

296

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

Protein sequence length:

403

The length of the canonical sequence.

Location on the sequence:

DIDEHTTPVEGSLSWTLGKR R RAAMDFPGAKVIVPQLKGRV

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                         DIDEHTTPVEGSLSWTLGKRRRAAMD----FPGAKVIVPQLKGRV-

                              DIDEHTTPVEGSLSWTLGKRRRAAMD----FPGASVIIAQL

Mouse                         DIDEHTTPVEGSLSWTLGKRRRIAMD----FPGAKIIVPQL

Bovine                        DIDEHTTPVEGSLSWTLGKRRRAAMD----FPGASVIVPQL

Chicken                       DIDESTTPVEAGLLWTLGKRRRTAMD----FPGAAIIMEQV

Slime mold                    DLNDDITPIEASLNWLISKRRREEGG----FPGASIIQKQL

Baker's yeast                 ELDESITPVEAALNWVISKSRRDLVDQKYWFNGYAKIMDQL

Fission yeast                 DIDDTTSPVEGSLSWIIGKRRRKEGG----FVGSSRILKEL

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	29 – 403	Aminomethyltransferase, mitochondrial
Helix	294 – 299

Literature citations

Nonketotic Hyperglycinemia: functional assessment of missense variants in GLDC to understand phenotypes of the disease.
Bravo-Alonso I.; Navarrete R.; Arribas-Carreira L.; Perona A.; Abia D.; Couce M.L.; Garcia-Cazorla A.; Morais A.; Domingo R.; Ramos M.A.; Swanson M.A.; Van Hove J.L.; Ugarte M.; Perez B.; Perez-Cerda C.; Rodriguez-Pombo P.;
Hum. Mutat. 38:678-691(2017)
Cited for: INVOLVEMENT IN NKH; VARIANTS NKH TRP-94; CYS-222 AND CYS-296;

UniProtKB/Swiss-Prot P48728: Variant p.Arg296Cys