UniProtKB/SwissProt variant VAR

Variant information

Variant position:

74

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 Leucine (L) to Serine (S) at position 74 (L74S, p.Leu74Ser).

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 hydrophobic (L) to small size and polar (S)

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:

Congenital disorder of glycosylation 1F (CDG1F) [MIM:609180]: A form of congenital disorder of glycosylation, a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. {ECO:0000269|PubMed:11733556, ECO:0000269|PubMed:11733564}. 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 CDG1F.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs104894589 [ dbSNP | Ensembl ]

Sequence information

Variant position:

74

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

Protein sequence length:

247

The length of the canonical sequence.

Location on the sequence:

SLLVKLPQVFKILGAKSAEG L SLQSVMLELVALTGTMVYSI

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                         SLLVKLPQVFKILGAKSAEGLSLQSVMLELVALTGTMVYSI

Mouse                         SLLVKLPQVFKLLGAKSAEGLSLQSVMLELVALTGTVVYSI

Caenorhabditis elegans        SILLFVPQILKIQAARSAQGISAASQLLALVGAIGTASYSY

Drosophila                    SVLVKVPQVLKILNSKSGEGINIVGVVLDLLAISFHLSYNF

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 – 247	Mannose-P-dolichol utilization defect 1 protein
Transmembrane	74 – 94	Helical
Domain	39 – 105	PQ-loop 1

Literature citations

A mutation in the human MPDU1 gene causes congenital disorder of glycosylation type If (CDG-If).
Kranz C.; Denecke J.; Lehrman M.A.; Ray S.; Kienz P.; Kreissel G.; Sagi D.; Peter-Katalinic J.; Freeze H.H.; Schmid T.; Jackowski-Dohrmann S.; Harms E.; Marquardt T.;
J. Clin. Invest. 108:1613-1619(2001)
Cited for: VARIANT CDG1F SER-74;

UniProtKB/Swiss-Prot O75352: Variant p.Leu74Ser