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SLC25A38 solute carrier family 25 member 38 [ Homo sapiens (human) ]

Gene ID: 54977, updated on 3-Apr-2024

Summary

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Official Symbol
SLC25A38provided by HGNC
Official Full Name
solute carrier family 25 member 38provided by HGNC
Primary source
HGNC:HGNC:26054
See related
Ensembl:ENSG00000144659 MIM:610819; AllianceGenome:HGNC:26054
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
SIDBA2
Summary
This gene is a member of the mitochondrial carrier family. The encoded protein is required during erythropoiesis and is important for the biosynthesis of heme. Mutations in this gene are the cause of autosomal congenital sideroblastic anemia (anemia, sideroblastic, 2, pyridoxine-refractory). A related pseudogene is found on chromosome 1. [provided by RefSeq, Aug 2017]
Expression
Ubiquitous expression in thyroid (RPKM 14.1), bone marrow (RPKM 11.1) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
3p22.1
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (39383370..39397351)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (39396296..39410278)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (39424861..39438842)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 24 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19703 Neighboring gene uncharacterized LOC105377037 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14225 Neighboring gene uncharacterized LOC105377644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19705 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19707 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:39445554-39446346 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:39447932-39448723 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:39450309-39451100 Neighboring gene ribosomal protein SA Neighboring gene small nucleolar RNA, H/ACA box 6 Neighboring gene small nucleolar RNA, H/ACA box 62

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. SLC25A38 as a novel biomarker for metastasis and clinical outcome in uveal melanoma. Fan Z, et al. Cell Death Dis, 2022 Apr 11. PMID 35411037, Free PMC Article
  2. SLC25A38 congenital sideroblastic anemia: Phenotypes and genotypes of 31 individuals from 24 families, including 11 novel mutations, and a review of the literature. Heeney MM, et al. Hum Mutat, 2021 Nov. PMID 34298585, Free PMC Article
  3. Clinical characterization and hematopoietic stem cell transplant outcomes for congenital sideroblastic anemia caused by a novel pathogenic variant in SLC25A38. Uminski K, et al. Pediatr Blood Cancer, 2020 Oct. PMID 32790119
  4. Novel frameshift variant (c.409dupG) in SLC25A38 is a common cause of congenital sideroblastic anaemia in the Indian subcontinent. Ravindra N, et al. J Clin Pathol, 2021 Mar. PMID 32605921
  5. Novel mutations in mitochondrial carrier family gene SLC25A38, causing congenital sideroblastic anemia in Iranian families, identified by whole exome sequencing. Mehri M, et al. Blood Cells Mol Dis, 2018 Jul. PMID 29499877

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SLC25A38 as a novel biomarker for metastasis and clinical outcome in uveal melanoma.
    Title: SLC25A38 as a novel biomarker for metastasis and clinical outcome in uveal melanoma.
  2. SLC25A38 congenital sideroblastic anemia: Phenotypes and genotypes of 31 individuals from 24 families, including 11 novel mutations, and a review of the literature.
    Title: SLC25A38 congenital sideroblastic anemia: Phenotypes and genotypes of 31 individuals from 24 families, including 11 novel mutations, and a review of the literature.
  3. Dentate gyrus volume deficit in schizophrenia.
    Title: Dentate gyrus volume deficit in schizophrenia.
  4. Novel frameshift variant (c.409dupG) in SLC25A38 is a common cause of congenital sideroblastic anaemia in the Indian subcontinent.
    Title: Novel frameshift variant (c.409dupG) in SLC25A38 is a common cause of congenital sideroblastic anaemia in the Indian subcontinent.
  5. Clinical characterization and hematopoietic stem cell transplant outcomes for congenital sideroblastic anemia caused by a novel pathogenic variant in SLC25A38.
    Title: Clinical characterization and hematopoietic stem cell transplant outcomes for congenital sideroblastic anemia caused by a novel pathogenic variant in SLC25A38.
  6. These findings suggest that sideroblastic anemia must be considered a possible etiology in cases with unexplained hemolytic anemia. Furthermore, mutations in SLC25A38 gene could be a prevalent cause of congenital sideroblastic anemia (CSA) in the Iranian population.
    Title: Novel mutations in mitochondrial carrier family gene SLC25A38, causing congenital sideroblastic anemia in Iranian families, identified by whole exome sequencing.
  7. report confirms the considerable variability in manifestations among patients with ALAS2 or SLC25A38 mutations and draws attention to differences in the assessment and the monitoring of iron overload and its complications
    Title: Non syndromic childhood onset congenital sideroblastic anemia: A report of 13 patients identified with an ALAS2 or SLC25A38 mutation.
  8. the biochemical and molecular characterization of yeast Hem25p and human SLC25A38, providing evidence that they are mitochondrial carriers for glycine. In particular, the hem25Delta mutant manifests a defect in the biosynthesis of delta-aminolevulinic acid and displays reduced levels of downstream heme and mitochondrial cytochromes.
    Title: Characterization of Human and Yeast Mitochondrial Glycine Carriers with Implications for Heme Biosynthesis and Anemia.
  9. Appoptosin can interact with mitochondrial outer-membrane fusion proteins and regulates mitochondrial morphology.
    Title: Appoptosin interacts with mitochondrial outer-membrane fusion proteins and regulates mitochondrial morphology.
  10. Given the tolerability of glycine and folate in humans, this study points to a potential novel treatment for SLC25A38 congenital sideroblastic anemia
    Title: Glycine and Folate Ameliorate Models of Congenital Sideroblastic Anemia.
Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Sideroblastic anemia 2
MedGen: C4225425 OMIM: 205950 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20551, FLJ22703

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables glycine transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables glycine transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in erythrocyte differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in glycine import into mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in glycine import into mitochondrion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in heme biosynthetic process TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in mitochondrial inner membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
mitochondrial glycine transporter
Names
appoptosin
mitochondrial glycine transporter GlyC

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_016931.1 RefSeqGene

    Range
    5047..19028
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1133

mRNA and Protein(s)

  1. NM_001354798.2 → NP_001341727.1  mitochondrial glycine transporter isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC099332, AC104850
    UniProtKB/TrEMBL
    A0A3B3IT77
    Conserved Domains (1) summary
    pfam00153
    Location:26 → 117
    Mito_carr; Mitochondrial carrier protein

  2. NM_017875.4 → NP_060345.2  mitochondrial glycine transporter isoform 1

    See identical proteins and their annotated locations for NP_060345.2

    Status: REVIEWED

    Source sequence(s)
    AA760706, AK000558, AK225388, DB113609
    Consensus CDS
    CCDS2685.1
    UniProtKB/Swiss-Prot
    A1LP07, Q96DW6, Q9NWX2
    UniProtKB/TrEMBL
    A0A2R8Y553
    Related
    ENSP00000497532.1, ENST00000650617.1
    Conserved Domains (1) summary
    pfam00153
    Location:26 → 117
    Mito_carr; Mitochondrial carrier protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    39383370..39397351
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047448413.1 → XP_047304369.1  mitochondrial glycine transporter isoform X2

    UniProtKB/TrEMBL
    A0A2R8Y823

  2. XM_047448414.1 → XP_047304370.1  mitochondrial glycine transporter isoform X2

    UniProtKB/TrEMBL
    A0A2R8Y823

  3. XM_047448415.1 → XP_047304371.1  mitochondrial glycine transporter isoform X2

    UniProtKB/TrEMBL
    A0A2R8Y823

  4. XM_011533869.3 → XP_011532171.1  mitochondrial glycine transporter isoform X1

    See identical proteins and their annotated locations for XP_011532171.1

    UniProtKB/TrEMBL
    A0A2R8Y553
    Conserved Domains (2) summary
    PTZ00168
    Location:22 → 274
    PTZ00168; mitochondrial carrier protein; Provisional
    pfam00153
    Location:20 → 111
    Mito_carr; Mitochondrial carrier protein

  5. XM_047448416.1 → XP_047304372.1  mitochondrial glycine transporter isoform X2

    UniProtKB/TrEMBL
    A0A2R8Y823

  6. XM_024453611.2 → XP_024309379.1  mitochondrial glycine transporter isoform X2

    UniProtKB/TrEMBL
    A0A2R8Y553, A0A2R8Y823
    Related
    ENSP00000496690.1, ENST00000645280.1
    Conserved Domains (1) summary
    pfam00153
    Location:8 → 99
    Mito_carr; Mitochondrial carrier protein

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    39396296..39410278
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054347026.1 → XP_054203001.1  mitochondrial glycine transporter isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96DW6.1 GenPept UniProtKB/Swiss-Prot:Q96DW6

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