UniProtKB/SwissProt variant VAR

Variant information

Variant position:

254

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

Type of variant:

US

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 Arginine (R) to Glycine (G) at position 254 (R254G, p.Arg254Gly).

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 large size and basic (R) to glycine (G)

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

Variant description:

In FRBRL; unknown pathological significance; loss of ceramidase activity.

Any additional useful information about the variant.

Sequence information

Variant position:

254

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

Protein sequence length:

395

The length of the canonical sequence.

Location on the sequence:

LGILEWILGKKDVMWIGFLT R TVLENSTSYEEAKNLLTKTK

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                         LGILEWILG-KKDVMWIGFLTRTVLENSTSYEEAKNLLTKTK

Chimpanzee                    LGILEWILG-KKDAMWIGFLTRTVLENSTSYEEAKNLLTKT

Mouse                         LGILEWMFG-RKDAQWVGFITRSVLENTTSYEEAKNTLTKT

Rat                           LGILEWMFG-KKNAQWVGFITRSVLENSTSYEEAKNILTKT

Bovine                        MGVMEWILG-KKDAQWVGFIIRSVLENSTSYEETKNILTKT

Caenorhabditis elegans        YGILKWVFGLEADGKWMSWLARETLETKTTYLDAKEHLMNT

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	143 – 395	Acid ceramidase subunit beta
Glycosylation	259 – 259	N-linked (GlcNAc...) asparagine
Disulfide bond	31 – 340	Interchain (between alpha and beta subunits)
Mutagenesis	259 – 259	N -> Q. Loss of ceramide catabolic process.
Helix	249 – 259

Literature citations

The human acid ceramidase gene (ASAH): structure, chromosomal location, mutation analysis, and expression.
Li C.M.; Park J.H.; He X.; Levy B.; Chen F.; Arai K.; Adler D.A.; Disteche C.M.; Koch J.; Sandhoff K.; Schuchman E.H.;
Genomics 62:223-231(1999)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; FUNCTION; CATALYTIC ACTIVITY; PATHWAY; VARIANTS FRBRL VAL-138; GLY-254 AND ARG-362; CHARACTERIZATION OF VARIANTS FRBRL VAL-138; GLY-254 AND ARG-362; TISSUE SPECIFICITY;

Brief Report: Peripheral Osteolysis in Adults Linked to ASAH1 (Acid Ceramidase) Mutations: A New Presentation of Farber's Disease.
Bonafe L.; Kariminejad A.; Li J.; Royer-Bertrand B.; Garcia V.; Mahdavi S.; Bozorgmehr B.; Lachman R.L.; Mittaz-Crettol L.; Campos-Xavier B.; Nampoothiri S.; Unger S.; Rivolta C.; Levade T.; Superti-Furga A.;
Arthritis Rheum. 68:2323-2327(2016)
Cited for: VARIANTS FRBRL ARG-169 AND GLY-254;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q13510: Variant p.Arg254Gly