UniProtKB/SwissProt variant VAR

Variant information

Variant position:

246

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 Valine (V) to Alanine (A) at position 246 (V246A, p.Val246Ala).

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 (V) to small size and hydrophobic (A)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

0

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 rs10103355 [ dbSNP | Ensembl ]

Sequence information

Variant position:

246

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:

RFSINGGYLGILEWILGKKD V MWIGFLTRTVLENSTSYEEA

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                         RFSINGGYLGILEWILG-KKDVMWIGFLTRTVLENSTSYEEA

Chimpanzee                    RFSINGGYLGILEWILG-KKDAMWIGFLTRTVLENSTSYEE

Mouse                         RFSINGGYLGILEWMFG-RKDAQWVGFITRSVLENTTSYEE

Rat                           RFSLNGGYLGILEWMFG-KKNAQWVGFITRSVLENSTSYEE

Bovine                        RFSIDGGFMGVMEWILG-KKDAQWVGFIIRSVLENSTSYEE

Caenorhabditis elegans        RFQLVGGYYGILKWVFGLEADGKWMSWLARETLETKTTYLD

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.

Literature citations

Molecular cloning and characterization of a full-length complementary DNA encoding human acid ceramidase. Identification of the first molecular lesion causing Farber disease.
Koch J.; Gaertner S.; Li C.M.; Quintern L.E.; Bernardo K.; Levran O.; Schnabel D.; Desnick R.J.; Schuchman E.H.; Sandhoff K.;
J. Biol. Chem. 271:33110-33115(1996)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); PARTIAL PROTEIN SEQUENCE; VARIANT FRBRL LYS-222; VARIANTS MET-72; VAL-93 AND ALA-246; GLYCOSYLATION; CATALYTIC ACTIVITY;

A new gene family predicted by a novel human heart cDNA.
Churchill J.R.; Wieland S.J.; Hoffman S.; Gallin E.K.; Murphy P.M.;
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANTS MET-72; VAL-93 AND ALA-246;

Human acid ceramidase gene: novel mutations in Farber disease.
Zhang Z.; Mandal A.K.; Mital A.; Popescu N.; Zimonjic D.; Moser A.; Moser H.; Mukherjee A.B.;
Mol. Genet. Metab. 70:301-309(2000)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS FRBRL HIS-22; ASP-23; VAL-138; LYS-222 AND ASP-320; VARIANTS MET-72; VAL-93 AND ALA-246;

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
The MGC Project Team;
Genome Res. 14:2121-2127(2004)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3); VARIANTS MET-72; VAL-93 AND ALA-246;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q13510: Variant p.Val246Ala