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UniProtKB/Swiss-Prot Q9GZU1: Variant p.Leu106Pro

Mucolipin-1
Gene: MCOLN1
Variant information

Variant position:  106
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 Proline (P) at position 106 (L106P, p.Leu106Pro).
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 medium size and hydrophobic.
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; decreases formation and extrusion of tubulo-vesicular structures when overexpressed; disrupts tetrameric assembly; abolishes lysosomal localization.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  106
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:   SNQLAVTFREENTIAFRHLF  L LGYSDGADDTFAAYTREQLY
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                         SNQLAVTFREENTIAFRHLFLLGYSDGADDTFAAYTREQLY

Mouse                         SNQLVVTFREENTIAFRHLFLLGYSDGSDDTFAAYTQEQLY

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.

TypePositionsDescription
Chain 1 – 580 Mucolipin-1
Topological domain 87 – 298 Extracellular
Mutagenesis 109 – 109 Y -> G. Abolishes formation and extrusion of tubulo-vesicular structures and decreases lysosomal exocytosis when overexpressed.
Mutagenesis 110 – 110 S -> C. Modulates ion conduction; when associoated with C-112 and C-113.
Mutagenesis 111 – 111 D -> Q. Modulates inhibition by Ca(2+) at different pH levels but does not abolish channel inward rectification; when associated with Q-114 and Q-115.
Mutagenesis 112 – 112 G -> C. Modulates ion conduction; when associoated with C-110 and C-113.
Mutagenesis 113 – 113 A -> C. Modulates ion conduction; when associoated with C-110 and C-112.
Mutagenesis 114 – 114 D -> Q. Modulates inhibition by Ca(2+) at different pH levels but does not abolish channel inward rectification; when associated with Q-111 and Q-115.
Mutagenesis 115 – 115 D -> Q. Modulates inhibition by Ca(2+) at different pH levels but does not abolish channel inward rectification; when associated with Q-111 and Q-114.


Literature citations

The cation channel mucolipin-1 is a bifunctional protein that facilitates membrane remodeling via its serine lipase domain.
LaPlante J.M.; Falardeau J.L.; Brown E.M.; Slaugenhaupt S.A.; Vassilev P.M.;
Exp. Cell Res. 317:691-705(2011)
Cited for: FUNCTION; MUTAGENESIS OF TYR-109; CHARACTERIZATION OF VARIANTS ML4 PRO-106 AND LEU-465;

Structural basis of dual Ca(2+)/pH regulation of the endolysosomal TRPML1 channel.
Li M.; Zhang W.K.; Benvin N.M.; Zhou X.; Su D.; Li H.; Wang S.; Michailidis I.E.; Tong L.; Li X.; Yang J.;
Nat. Struct. Mol. Biol. 24:205-213(2017)
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 84-296; EXTRACELLULAR/LUMENAL PORE-FORMING DOMAIN; SUBUNIT; ACTIVITY REGULATION; MUTAGENESIS OF SER-110; ASP-111; GLY-112; ALA-113; ASP-114; ASP-115; LEU-144; ARG-146 AND VAL-432; CHARACTERIZATION OF VARIANTS ML4 PRO-106 AND PRO-232;

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;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.