UniProtKB/SwissProt variant VAR

Variant information

Variant position:

362

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 Aspartate (D) to Tyrosine (Y) at position 362 (D362Y, p.Asp362Tyr).

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 acidic (D) to large size and aromatic (Y)

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:

Mucolipidosis 4 (ML4) [MIM:252650]: An autosomal recessive lysosomal storage disorder characterized by severe psychomotor retardation and ophthalmologic abnormalities, including corneal opacity, retinal degeneration and strabismus. Storage bodies of lipids and water-soluble substances are seen by electron microscopy in almost every cell type of the patients. Most patients are unable to speak or walk independently and reach a maximal developmental level of 1-2 years. All patients have constitutive achlorhydia associated with a secondary elevation of serum gastrin levels. {ECO:0000269|PubMed:10973263, ECO:0000269|PubMed:11013137, ECO:0000269|PubMed:11030752, ECO:0000269|PubMed:11317355, ECO:0000269|PubMed:12182165, ECO:0000269|PubMed:14749347, ECO:0000269|PubMed:15178326, ECO:0000269|PubMed:15523648, ECO:0000269|PubMed:16978393, ECO:0000269|PubMed:18794901, ECO:0000269|PubMed:21256127, ECO:0000269|PubMed:28112729}. 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 ML4; affects channel activity; abolishes Fe(2+) permeability.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs121908372 [ dbSNP | Ensembl ]

Sequence information

Variant position:

362

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

Protein sequence length:

580

The length of the canonical sequence.

Location on the sequence:

ISLWERLEFVNGWYILLVTS D VLTISGTIMKIGIEAKNLAS

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                         ISLWERLEFVNGWYILLVTSDVLTISGTIMKIGIEAKNLAS

Mouse                         ISLWERLEFVNGWYILLVTSDVLTISGTVMKIGIEAKNLAS

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	1 – 580	Mucolipin-1
Transmembrane	351 – 371	Helical; Name=3
Helix	353 – 377

Literature citations

Mucolipidosis type IV is caused by mutations in a gene encoding a novel transient receptor potential channel.
Sun M.; Goldin E.; Stahl S.; Falardeau J.L.; Kennedy J.C.; Acierno J.S. Jr.; Bove C.; Kaneski C.R.; Nagle J.; Bromley M.C.; Colman M.; Schiffmann R.; Slaugenhaupt S.A.;
Hum. Mol. Genet. 9:2471-2478(2000)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA]; TISSUE SPECIFICITY; VARIANTS ML4 TYR-362; PHE-408 DEL AND LEU-446;

Molecular pathophysiology of mucolipidosis type IV: pH dysregulation of the mucolipin-1 cation channel.
Raychowdhury M.K.; Gonzalez-Perrett S.; Montalbetti N.; Timpanaro G.A.; Chasan B.; Goldmann W.H.; Stahl S.; Cooney A.; Goldin E.; Cantiello H.F.;
Hum. Mol. Genet. 13:617-627(2004)
Cited for: FUNCTIONAL CHARACTERIZATION; SUBUNIT; CHARACTERIZATION OF VARIANTS ML4 TYR-362; PHE-408 DEL AND LEU-446;

The type IV mucolipidosis-associated protein TRPML1 is an endolysosomal iron release channel.
Dong X.P.; Cheng X.; Mills E.; Delling M.; Wang F.; Kurz T.; Xu H.;
Nature 455:992-996(2008)
Cited for: FUNCTION; MUTAGENESIS OF VAL-432; CHARACTERIZATION OF VARIANTS ML4 PRO-232; TYR-362; CYS-403 AND LEU-446;

The neurogenetics of mucolipidosis type IV.
Altarescu G.; Sun M.; Moore D.F.; Smith J.A.; Wiggs E.A.; Solomon B.I.; Patronas N.J.; Frei K.P.; Gupta S.; Kaneski C.R.; Quarrell O.W.; Slaugenhaupt S.A.; Goldin E.; Schiffmann R.;
Neurology 59:306-313(2002)
Cited for: VARIANTS ML4 PRO-106; TYR-362; PHE-408 DEL AND PRO-447;

UniProtKB/Swiss-Prot Q9GZU1: Variant p.Asp362Tyr