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MFSD2A major facilitator superfamily domain containing 2A [ Homo sapiens (human) ]

Gene ID: 84879, updated on 9-Jun-2020

Summary

Official Symbol
MFSD2Aprovided by HGNC
Official Full Name
major facilitator superfamily domain containing 2Aprovided by HGNC
Primary source
HGNC:HGNC:25897
See related
Ensembl:ENSG00000168389 MIM:614397
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NLS1; MFSD2; MCPH15
Summary
The protein encoded by this gene is a transmembrane protein and sodium-dependent lysophosphatidylcholine transporter. The encoded protein is involved in the establishment of the blood-brain barrier and is required for brain growth and function. Defects in this gene are a cause of a progressive microcephaly syndrome. [provided by RefSeq, Mar 2017]
Expression
Broad expression in testis (RPKM 27.5), lung (RPKM 23.6) and 14 other tissues See more
Orthologs

Genomic context

See MFSD2A in Genome Data Viewer
Location:
1p34.2
Exon count:
14
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (39955112..39969968)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (40420784..40435630)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene tRNA isopentenyltransferase 1 Neighboring gene Sharpr-MPRA regulatory region 6057 Neighboring gene MYCL antisense RNA 1 Neighboring gene MYCL proto-oncogene, bHLH transcription factor Neighboring gene ribosomal protein S2 pseudogene 12 Neighboring gene uncharacterized LOC105378669 Neighboring gene cyclase associated actin cytoskeleton regulatory protein 1 Neighboring gene palmitoyl-protein thioesterase 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Primary autosomal recessive microcephaly 15
MedGen: C4225310 OMIM: 616486 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Generalization of variants identified by genome-wide association studies for electrocardiographic traits in African Americans.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ14490, FLJ35904

Gene Ontology Provided by GOA

Function Evidence Code Pubs
fatty acid transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
long-chain fatty acid transporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
long-chain fatty acid transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 
lysophospholipid transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lysophospholipid transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
oleate transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
phospholipid transporter activity TAS
Traceable Author Statement
more info
 
symporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 
transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
brain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
brain development ISS
Inferred from Sequence or Structural Similarity
more info
 
carbohydrate transport IEA
Inferred from Electronic Annotation
more info
 
cellular response to starvation ISS
Inferred from Sequence or Structural Similarity
more info
 
cognition IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT embryonic brain development ISS
Inferred from Sequence or Structural Similarity
more info
 
energy homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
establishment of blood-brain barrier ISS
Inferred from Sequence or Structural Similarity
more info
 
NOT establishment of blood-brain barrier ISS
Inferred from Sequence or Structural Similarity
more info
 
NOT establishment of blood-retinal barrier ISS
Inferred from Sequence or Structural Similarity
more info
 
establishment of endothelial blood-brain barrier ISS
Inferred from Sequence or Structural Similarity
more info
 
fatty acid transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
fatty acid transport ISS
Inferred from Sequence or Structural Similarity
more info
 
hippocampus development ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
lipid transport across blood brain barrier IMP
Inferred from Mutant Phenotype
more info
PubMed 
lipid transport across blood brain barrier ISS
Inferred from Sequence or Structural Similarity
more info
 
long-chain fatty acid transport ISS
Inferred from Sequence or Structural Similarity
more info
 
lysophospholipid transport IDA
Inferred from Direct Assay
more info
PubMed 
lysophospholipid transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
maintenance of permeability of blood-brain barrier ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
motor behavior ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of fatty acid beta-oxidation ISS
Inferred from Sequence or Structural Similarity
more info
 
organic substance transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylcholine biosynthetic process TAS
Traceable Author Statement
more info
 
photoreceptor cell morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
photoreceptor cell outer segment organization ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cell growth ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of rhodopsin gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of triglyceride biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of dendrite development ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of multicellular organism growth ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of neuron projection arborization ISS
Inferred from Sequence or Structural Similarity
more info
 
retina morphogenesis in camera-type eye ISS
Inferred from Sequence or Structural Similarity
more info
 
retinal pigment epithelium development ISS
Inferred from Sequence or Structural Similarity
more info
 
transcytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
very-low-density lipoprotein particle assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane TAS
Traceable Author Statement
more info
PubMed 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
integral component of plasma membrane RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
sodium-dependent lysophosphatidylcholine symporter 1
Names
major facilitator superfamily domain-containing protein 2A
sodium-dependent LPC symporter 1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_053084.1 RefSeqGene

    Range
    5034..19845
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001136493.3NP_001129965.1  sodium-dependent lysophosphatidylcholine symporter 1 isoform 1

    See identical proteins and their annotated locations for NP_001129965.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK093223, BP321361, DB376308
    Consensus CDS
    CCDS44118.1
    UniProtKB/Swiss-Prot
    Q8NA29
    UniProtKB/TrEMBL
    Q71RE4
    Related
    ENSP00000361895.5, ENST00000372809.5
    Conserved Domains (2) summary
    pfam13347
    Location:46509
    MFS_2; MFS/sugar transport protein
    cl21472
    Location:40511
    MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
  2. NM_001287808.1NP_001274737.1  sodium-dependent lysophosphatidylcholine symporter 1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in its 5' UTR, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AF370364, AK093223, BP321361, DB376308
    Consensus CDS
    CCDS72762.1
    UniProtKB/Swiss-Prot
    Q8NA29
    UniProtKB/TrEMBL
    E7EPI8, Q71RE4
    Related
    ENSP00000391261.2, ENST00000420632.6
    Conserved Domains (2) summary
    pfam13347
    Location:3340
    MFS_2; MFS/sugar transport protein
    cl21472
    Location:1342
    MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
  3. NM_001287809.2NP_001274738.1  sodium-dependent lysophosphatidylcholine symporter 1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (4) is shorter, compared to isoform 1.
    Source sequence(s)
    AB073383, AK297991, DB376308, DC297497
    UniProtKB/Swiss-Prot
    Q8NA29
    UniProtKB/TrEMBL
    B4DNN7, Q71RE4
    Conserved Domains (2) summary
    pfam13347
    Location:32457
    MFS_2; MFS/sugar transport protein
    cl21472
    Location:51459
    MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
  4. NM_001349821.2NP_001336750.1  sodium-dependent lysophosphatidylcholine symporter 1 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) encodes isoform 6.
    Source sequence(s)
    AL663070
    Conserved Domains (1) summary
    pfam13347
    Location:46494
    MFS_2; MFS/sugar transport protein
  5. NM_001349822.2NP_001336751.1  sodium-dependent lysophosphatidylcholine symporter 1 isoform 7

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) encodes isoform 7.
    Source sequence(s)
    AL663070
    Conserved Domains (1) summary
    pfam13347
    Location:48468
    MFS_2; MFS/sugar transport protein
  6. NM_001349823.2NP_001336752.1  sodium-dependent lysophosphatidylcholine symporter 1 isoform 8

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) encodes isoform 8.
    Source sequence(s)
    AL663070
    Conserved Domains (1) summary
    pfam13347
    Location:2381
    MFS_2; MFS/sugar transport protein
  7. NM_032793.5NP_116182.2  sodium-dependent lysophosphatidylcholine symporter 1 isoform 2

    See identical proteins and their annotated locations for NP_116182.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AB073383, BP321361, DB376308
    Consensus CDS
    CCDS446.1
    UniProtKB/Swiss-Prot
    Q8NA29
    UniProtKB/TrEMBL
    Q71RE4
    Related
    ENSP00000361898.5, ENST00000372811.9
    Conserved Domains (1) summary
    pfam13347
    Location:48496
    MFS_2; MFS/sugar transport protein

RNA

  1. NR_109896.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB073383, BP321361, DB376308
    Related
    ENST00000483824.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    39955112..39969968
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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