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SLC38A8 solute carrier family 38 member 8 [ Homo sapiens (human) ]

Gene ID: 146167, updated on 27-Nov-2024

Summary

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Official Symbol
SLC38A8provided by HGNC
Official Full Name
solute carrier family 38 member 8provided by HGNC
Primary source
HGNC:HGNC:32434
See related
Ensembl:ENSG00000166558 MIM:615585; AllianceGenome:HGNC:32434
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
FVH2; FHASD; SNAT8
Summary
This gene encodes a putative sodium-dependent amino-acid/proton antiporter. The protein has eleven transmembrane domains, an extracellular N-terminus and an intracellular C-terminal tail. The protein is a member of the SLC38 sodium-coupled neutral amino acid transporter family of proteins. Mutations in this gene result in foveal hypoplasia with or without optic nerve misrouting and/or anterior segment dysgenesis. [provided by RefSeq, May 2014]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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See SLC38A8 in Genome Data Viewer
Location:
16q23.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (84009667..84043372, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (90075718..90109442, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (84043272..84076400, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene malonyl-CoA decarboxylase Neighboring gene uncharacterized LOC105371372 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83987658-83988427 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7772 Neighboring gene oxidative stress induced growth inhibitor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84007063-84007564 Neighboring gene Sharpr-MPRA regulatory region 13657 Neighboring gene N-terminal EF-hand calcium binding protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7773 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84035929-84036711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84050003-84050504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84060729-84061230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84066580-84067080 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84075154-84075858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84075859-84076562 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:84076563-84077267 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:84077268-84077971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84078959-84079731 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84082148-84083032 Neighboring gene RNA, 5S ribosomal pseudogene 432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84088845-84089438 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84089439-84090031 Neighboring gene membrane bound transcription factor peptidase, site 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7775 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:84125154-84126353 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11232 Neighboring gene MBTPS1 divergent transcript

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. The Phenotypic and Mutational Spectrum of the FHONDA Syndrome and Oculocutaneous Albinism: Similarities and Differences. Kruijt CC, et al. Invest Ophthalmol Vis Sci, 2022 Jan 3. PMID 35029636, Free PMC Article
  2. Novel Biallelic Variants and Phenotypic Features in Patients with SLC38A8-Related Foveal Hypoplasia. Schiff ER, et al. Int J Mol Sci, 2021 Jan 24. PMID 33498813, Free PMC Article
  3. The pathogenicity of SLC38A8 in five families with foveal hypoplasia and congenital nystagmus. Weiner C, et al. Exp Eye Res, 2020 Apr. PMID 32032626
  4. Recessive mutations in SLC38A8 cause foveal hypoplasia and optic nerve misrouting without albinism. Poulter JA, et al. Am J Hum Genet, 2013 Dec 5. PMID 24290379, Free PMC Article
  5. Gene-environment interaction effects on lung function- a genome-wide association study within the Framingham heart study. Liao SY, et al. Environ Health, 2013 Dec 1. PMID 24289273, Free PMC Article

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The Phenotypic and Mutational Spectrum of the FHONDA Syndrome and Oculocutaneous Albinism: Similarities and Differences.
    Title: The Phenotypic and Mutational Spectrum of the FHONDA Syndrome and Oculocutaneous Albinism: Similarities and Differences.
  2. Genetic causes of nystagmus, foveal hypoplasia and subnormal visual acuity- other than albinism.
    Title: Genetic causes of nystagmus, foveal hypoplasia and subnormal visual acuity- other than albinism.
  3. SLC38A8 mutations result in arrested retinal development with loss of cone photoreceptor specialization.
    Title: SLC38A8 mutations result in arrested retinal development with loss of cone photoreceptor specialization.
  4. Novel Biallelic Variants and Phenotypic Features in Patients with SLC38A8-Related Foveal Hypoplasia.
    Title: Novel Biallelic Variants and Phenotypic Features in Patients with SLC38A8-Related Foveal Hypoplasia.
  5. The pathogenicity of SLC38A8 in five families with foveal hypoplasia and congenital nystagmus.
    Title: The pathogenicity of SLC38A8 in five families with foveal hypoplasia and congenital nystagmus.
  6. Study found that SNP rs9931086 in the SLC38A8 gene and genes CTLA-4, HDAC, and PPAR-alpha, which are involved in inflammatory processes, may modify the effects of occupational exposure on lung function.
    Title: Gene-environment interaction effects on lung function- a genome-wide association study within the Framingham heart study.
  7. Isolated foveal hypoplasia with secondary nystagmus and low vision is associated with a homozygous SLC38A8 mutation.
    Title: Isolated foveal hypoplasia with secondary nystagmus and low vision is associated with a homozygous SLC38A8 mutation.
  8. Recessive mutations in SLC38A8 cause foveal hypoplasia and optic nerve misrouting without albinism.
    Title: Recessive mutations in SLC38A8 cause foveal hypoplasia and optic nerve misrouting without albinism.
  9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Foveal hypoplasia - optic nerve decussation defect - anterior segment dysgenesis syndrome
MedGen: C3807873 OMIM: 609218 GeneReviews: Not available
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EBI GWAS Catalog

Description
Association between liver-specific gene polymorphisms and their expression levels with nonalcoholic fatty liver disease.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

General gene information

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Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables L-amino acid transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in L-alpha-amino acid transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in amino acid transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron projection development IEA
Inferred from Electronic Annotation
more info
  
involved_in optic nerve development IEA
Inferred from Electronic Annotation
more info
  
involved_in retinal pigment epithelium development IEA
Inferred from Electronic Annotation
more info
  
involved_in visual perception IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in axon IEA
Inferred from Electronic Annotation
more info
  
located_in cell cortex IEA
Inferred from Electronic Annotation
more info
  
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
solute carrier family 38 member 8
Names
amino acid transporter SLC38A8
putative sodium-coupled neutral amino acid transporter 8

NCBI Reference Sequences (RefSeq)

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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_034136.1 RefSeqGene

    Range
    4363..37491
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001080442.3 → NP_001073911.1  solute carrier family 38 member 8

    See identical proteins and their annotated locations for NP_001073911.1

    Status: REVIEWED

    Source sequence(s)
    AC040169
    Consensus CDS
    CCDS32495.1
    UniProtKB/Swiss-Prot
    A6NNN8
    Related
    ENSP00000299709.3, ENST00000299709.8
    Conserved Domains (2) summary
    COG0814
    Location:23 → 431
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:23 → 431
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    84009667..84043372 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017022946.1 → XP_016878435.1  solute carrier family 38 member 8 isoform X1

    UniProtKB/Swiss-Prot
    A6NNN8
    Conserved Domains (2) summary
    COG0814
    Location:23 → 431
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:23 → 431
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    90075718..90109442 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054379629.1 → XP_054235604.1  solute carrier family 38 member 8 isoform X1

    UniProtKB/Swiss-Prot
    A6NNN8
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A6NNN8.1 GenPept UniProtKB/Swiss-Prot:A6NNN8

Gene LinkOut

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