UniProtKB/SwissProt variant VAR

Variant information

Variant position:

339

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 Arginine (R) to Histidine (H) at position 339 (R339H, p.Arg339His).

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 medium size and polar (H)

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

Variant description:

In NEDMISBA; reduced expression; no effect on cell membrane localization; no effect on LPC transport activity.

Any additional useful information about the variant.

Sequence information

Variant position:

339

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

Protein sequence length:

543

The length of the canonical sequence.

Location on the sequence:

LAFMLVEGNFVLFCTYTLGF R NEFQNLLLAIMLSATLTIPI

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                         LAFMLVEGNFVLFCTYTLGFRNEFQNLLLAIMLSATLTIPI

Mouse                         LAFMLVEGNFALFCTYTLDFRNEFQNLLLAIMLSATFTIPI

Xenopus tropicalis            LAFMLLEGNFALFLTYTMGFRRDFQNILLVVMLSATLTVPF

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	1 – 543	Sodium-dependent lysophosphatidylcholine symporter 1
Topological domain	334 – 344	Extracellular
Disulfide bond	225 – 473
Mutagenesis	325 – 325	E -> ADQR. Abolished lysophosphatidylcholine (LPC) transport.
Mutagenesis	328 – 328	F -> AY. Reduced lysophosphatidylcholine (LPC) transport.
Mutagenesis	334 – 334	Y -> A. Does not affect lysophosphatidylcholine (LPC) transport.
Mutagenesis	339 – 339	R -> A. Reduced lysophosphatidylcholine (LPC) transport.
Mutagenesis	342 – 342	F -> A. Abolished lysophosphatidylcholine (LPC) transport.
Mutagenesis	346 – 346	L -> A. Abolished lysophosphatidylcholine (LPC) transport.
Mutagenesis	349 – 349	I -> A. Reduced lysophosphatidylcholine (LPC) transport.
Mutagenesis	350 – 350	M -> A. Reduced lysophosphatidylcholine (LPC) transport.
Mutagenesis	357 – 357	I -> A. Does not affect lysophosphatidylcholine (LPC) transport.
Mutagenesis	357 – 357	I -> W. Abolished lysophosphatidylcholine (LPC) transport.

Literature citations

Biallelic MFSD2A variants associated with congenital microcephaly, developmental delay, and recognizable neuroimaging features.
Scala M.; Chua G.L.; Chin C.F.; Alsaif H.S.; Borovikov A.; Riazuddin S.; Riazuddin S.; Chiara Manzini M.; Severino M.; Kuk A.; Fan H.; Jamshidi Y.; Toosi M.B.; Doosti M.; Karimiani E.G.; Salpietro V.; Dadali E.; Baydakova G.; Konovalov F.; Lozier E.; O'Connor E.; Sabr Y.; Alfaifi A.; Ashrafzadeh F.; Striano P.; Zara F.; Alkuraya F.S.; Houlden H.; Maroofian R.; Silver D.L.;
Eur. J. Hum. Genet. 28:1509-1519(2020)
Cited for: VARIANTS NEDMISBA MET-172; MET-211; PHE-263; HIS-339 AND LEU-506; CHARACTERIZATION OF VARIANTS MET-211; PHE-263; HIS-339 AND LEU-506; MUTAGENESIS OF PRO-177; FUNCTION; SUBCELLULAR LOCATION;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q8NA29: Variant p.Arg339His