UniProtKB/SwissProt variant VAR

Variant information

Variant position:

113

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

Type of variant:

LP/P [Disclaimer]

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 Asparagine (N) to Aspartate (D) at position 113 (N113D, p.Asn113Asp).

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 polar (N) to medium size and acidic (D)

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

BLOSUM score:

1

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 HLD18; decreased function in sphingolipid biosynthetic process.

Any additional useful information about the variant.

Sequence information

Variant position:

113

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

Protein sequence length:

323

The length of the canonical sequence.

Location on the sequence:

HNAAFGNCKAMWNRWFGMFA N LPIGIPYSISFKRYHMDHHR

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                         HNAAFGNCKAMWNRWFGMFANLPIGIPYSISFKRYHMDHHR

Mouse                         HNFPFGHHKALWNRWFGMFANLSLGVPYSISFKRYHMDHHR

Rat                           HNFPFGHHKAMWNRWFGMFANLSLGVPYSISFKRYHMDHHR

Bovine                        HNSAFGHYKAMWNRWFGIFANLPIGVPYSVSFKRYHMDHHR

Chicken                       HNSAFGNGRAMWNRWFGIFANLPLGLPYSISFKRYHMDHHR

Xenopus tropicalis            HNSAFGNSKAMWNRCFGMFANLPLGLPYSVSFKRYHMDHHR

Caenorhabditis elegans        HNQAFGTNRPLANRIFGFIANLPMCIPMSISFKKYHLEHHR

Drosophila                    HNLAFGHSRPMHNRILGFICNLPIGLPMSISFKKYHLEHHR

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	2 – 323	Sphingolipid delta(4)-desaturase DES1
Transmembrane	102 – 122	Helical

Literature citations

Loss of the sphingolipid desaturase DEGS1 causes hypomyelinating leukodystrophy.
Pant D.C.; Dorboz I.; Schluter A.; Fourcade S.; Launay N.; Joya J.; Aguilera-Albesa S.; Yoldi M.E.; Casasnovas C.; Willis M.J.; Ruiz M.; Ville D.; Lesca G.; Siquier-Pernet K.; Desguerre I.; Yan H.; Wang J.; Burmeister M.; Brady L.; Tarnopolsky M.; Cornet C.; Rubbini D.; Terriente J.; James K.N.; Musaev D.; Zaki M.S.; Patterson M.C.; Lanpher B.C.; Klee E.W.; Pinto e Vairo F.; Wohler E.; Sobreira N.L.M.; Cohen J.S.; Maroofian R.; Galehdari H.; Mazaheri N.; Shariati G.; Colleaux L.; Rodriguez D.; Gleeson J.G.; Pujades C.; Fatemi A.; Boespflug-Tanguy O.; Pujol A.;
J. Clin. Invest. 129:1240-1256(2019)
Cited for: FUNCTION; INVOLVEMENT IN HLD18; VARIANTS HLD18 THR-37; 107-TRP--GLU-323 DEL; ASP-113; ARG-132; TRP-133; 173-ARG--GLU-323 DEL; ASP-189; SER-255; 284-TYR--GLU-323 DEL; 293-TRP--GLU-323 DEL AND GLU-323 DEL; CHARACTERIZATION OF VARIANTS HLD18 ASP-113 AND SER-255;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O15121: Variant p.Asn113Asp