UniProtKB/SwissProt variant VAR

Variant information

Variant position:

294

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

Type of variant:

LB/B

The variants are classified into three categories: LP/P, LB/B and US.

LP/P: likely pathogenic or pathogenic.
LB/B: likely benign or benign.
US: uncertain significance

Residue change:

From Serine (S) to Phenylalanine (F) at position 294 (S294F, p.Ser294Phe).

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 small size and polar (S) to large size and aromatic (F)

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

Other resources:

Links to websites of interest for the variant.

Variant rs35499907 [ dbSNP | Ensembl ]

Sequence information

Variant position:

294

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

Protein sequence length:

572

The length of the canonical sequence.

Location on the sequence:

LNYSTINYKWSFGDNTGLFV S TNHTVNHTYVLNGTFSLNLT

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                         LNYSTINYKWSFGDNTGLFVSTNHTVNHTYVLNGTFSLNLT

Mouse                         LNDSAISYKWNFGDNTGLFVSNNHTLNHTYVLNGTFNLNLT

Rat                           LNYSAISYKWNFGDNTGLFVSNNHTLNHTYVLNGTFNFNLT

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	23 – 572	Transmembrane glycoprotein NMB
Topological domain	23 – 498	Extracellular
Domain	240 – 327	PKD
Glycosylation	275 – 275	N-linked (GlcNAc...) asparagine
Glycosylation	296 – 296	N-linked (GlcNAc...) asparagine
Glycosylation	300 – 300	N-linked (GlcNAc...) asparagine
Glycosylation	306 – 306	N-linked (GlcNAc...) asparagine
Glycosylation	312 – 312	N-linked (GlcNAc...) asparagine

Literature citations

Loss of GPNMB Causes Autosomal-Recessive Amyloidosis Cutis Dyschromica in Humans.
Yang C.F.; Lin S.P.; Chiang C.P.; Wu Y.H.; H'ng W.S.; Chang C.P.; Chen Y.T.; Wu J.Y.;
Am. J. Hum. Genet. 102:219-232(2018)
Cited for: INVOLVEMENT IN PLCA3; VARIANTS PLCA3 189-ARG--SER-572 DEL AND 220-TYR--SER-572 DEL; CHARACTERIZATION OF VARIANT PLCA3 189-ARG--SER-572 DEL; SUBCELLULAR LOCATION; TISSUE SPECIFICITY; VARIANT PHE-294;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q14956: Variant p.Ser294Phe