UniProtKB/SwissProt variant VAR

Variant information

Variant position:

253

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 Lysine (K) to Arginine (R) at position 253 (K253R, p.Lys253Arg).

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:

Similar physico-chemical property. Both residues are large size and basic.

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

Involvement in disease:

Mitochondrial complex I deficiency, nuclear type 11 (MC1DN11) [MIM:618234]: A form of mitochondrial complex I deficiency, the most common biochemical signature of mitochondrial disorders, a group of highly heterogeneous conditions characterized by defective oxidative phosphorylation, which collectively affects 1 in 5-10000 live births. Clinical disorders have variable severity, ranging from lethal neonatal disease to adult-onset neurodegenerative disorders. Phenotypes include macrocephaly with progressive leukodystrophy, non-specific encephalopathy, cardiomyopathy, myopathy, liver disease, Leigh syndrome, Leber hereditary optic neuropathy, and some forms of Parkinson disease. MC1DN11 transmission pattern is consistent with autosomal recessive inheritance. {ECO:0000269|PubMed:17557076, ECO:0000269|PubMed:21931170}. 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 MC1DN11; due to a nucleotide substitution located in the splice site consensus sequence at the end of exon 3; patient cells contain normally spliced transcripts corresponding to protein variant R-253 but also transcripts lacking the final 6 base pairs of exon 3 and corresponding to protein variant 252-VK-253 del.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs387906957 [ dbSNP | Ensembl ]

Sequence information

Variant position:

253

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

Protein sequence length:

327

The length of the canonical sequence.

Location on the sequence:

TNQMYSYFMFTRGGPYWQEV K IPFSKFFFSNRGRIRDVQHE

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                         TNQMYSYFMFTRGGPYWQEVKIPFSKFFFSNRGRIRDVQHE

Gorilla                       TNQMYSYFMFTRGGPYWQEVKIPFSKFFFSNRGRIRDVQHE

Chimpanzee                    TNQMYSYFMFTRGGPYWQEVKIPFSKFFFSNRGRIRDVQHE

Mouse                         KNQMYSYFMFTRGGPYWQEVKIPFSKFFFSNQGRVRDVQGP

Caenorhabditis elegans        WGDSFSHPLHTHGGPYWQYEKIPFSKFFHTVAGRIQDRQYR

Drosophila                    WNDIYHYVLYTRGGPHWQIAKIPFSKFFLSSKGRVQDRQGA

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	25 – 327	Complex I intermediate-associated protein 30, mitochondrial

Literature citations

Human CIA30 is involved in the early assembly of mitochondrial complex I and mutations in its gene cause disease.
Dunning C.J.; McKenzie M.; Sugiana C.; Lazarou M.; Silke J.; Connelly A.; Fletcher J.M.; Kirby D.M.; Thorburn D.R.; Ryan M.T.;
EMBO J. 26:3227-3237(2007)
Cited for: FUNCTION; SUBCELLULAR LOCATION; SUBUNIT; INVOLVEMENT IN MC1DN11; VARIANTS MC1DN11 PRO-207; 252-VAL-LYS-253 DEL AND ARG-253;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9Y375: Variant p.Lys253Arg