Home  |  Contact

UniProtKB/Swiss-Prot Q8NA29: Variant p.Arg339His

Sodium-dependent lysophosphatidylcholine symporter 1
Gene: MFSD2A
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.

TypePositionsDescription
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;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.