SLC29A3 solute carrier family 29 member 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC29A3provided by HGNC
Official Full Name: solute carrier family 29 member 3provided by HGNC
Primary source: HGNC:HGNC:23096
See related: Ensembl:ENSG00000198246 MIM:612373; AllianceGenome:HGNC:23096
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: ENT3; HJCD; PHID; HCLAP
Summary: This gene encodes a nucleoside transporter. The encoded protein plays a role in cellular uptake of nucleosides, nucleobases, and their related analogs. Mutations in this gene have been associated with H syndrome, which is characterized by cutaneous hyperpigmentation and hypertrichosis, hepatosplenomegaly, heart anomalies, and hypogonadism. A related disorder, PHID (pigmented hypertrichosis with insulin-dependent diabetes mellitus), has also been associated with mutations at this locus. Alternatively spliced transcript variants have been described.[provided by RefSeq, Mar 2010]
Expression: Ubiquitous expression in placenta (RPKM 7.5), urinary bladder (RPKM 5.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q22.1

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (71319259..71381423)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (72188806..72250962)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (73079016..73123142)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of Coding Variants in 10q22.1 Associated with Vitiligo in the Chinese Han Population.
Title: Identification of Coding Variants in 10q22.1 Associated with Vitiligo in the Chinese Han Population.
Equilibrative nucleotide transporter ENT3 (SLC29A3): A unique transporter for inherited disorders and cancers.
Title: Equilibrative nucleotide transporter ENT3 (SLC29A3): A unique transporter for inherited disorders and cancers.
Loss of function of ENT3 drives histiocytosis and inflammation through TLR-MAPK signaling.
Title: Loss of function of ENT3 drives histiocytosis and inflammation through TLR-MAPK signaling.
Phenotypic intrafamilial variability including H syndrome and Rosai-Dorfman disease associated with the same c.1088G > A mutation in the SLC29A3 gene.
Title: Phenotypic intrafamilial variability including H syndrome and Rosai-Dorfman disease associated with the same c.1088G > A mutation in the SLC29A3 gene.
Resolution of sclerotic lesions of dysosteosclerosis due to biallelic SLC29A3 variant in a Turkish girl.
Title: Resolution of sclerotic lesions of dysosteosclerosis due to biallelic SLC29A3 variant in a Turkish girl.
MiR-1224-5p acts as a tumor suppressor via inhibiting the malignancy of rectal cancer through targeting SLC29A3.
Title: MiR-1224-5p acts as a tumor suppressor via inhibiting the malignancy of rectal cancer through targeting SLC29A3.
Pediatric recurrent Rosai-Dorfman disease with germline heterozygous SLC29A3 and somatic MAP2K1 mutations.
Title: Pediatric recurrent Rosai-Dorfman disease with germline heterozygous SLC29A3 and somatic MAP2K1 mutations.
A novel 3'UTR mutation in the SLC29A3 gene is associated with the PHID (Pigmentary Hypertrichosis and non-autoimmune insulin-dependent diabetes mellitus) syndrome, highlighting a potentially new pathological mechanism for this disease. The involvement of the 3'UTR has not been previously established in any of the H syndrome disease cluster or in any complex syndrome of DM (Diabetes Mellitus).
Title: A novel 3' untranslated region mutation in the SLC29A3 gene associated with pigmentary hypertrichosis and non-autoimmune insulin-dependent diabetes mellitus syndrome.
mutations in SLC29A3 and TCIRG1 in patients with Sclerosing bone dysplasias with hallmarks of dysosteosclerosis.
Title: Sclerosing bone dysplasias with hallmarks of dysosteosclerosis in four patients carrying mutations in SLC29A3 and TCIRG1.
The SLC29A3 gene, encoding a nucleoside transporter protein, is found in intracellular membranes. Mutations in this gene cause a wide range of clinical manifestations including H syndrome, pigmented hypertrichosis with insulin dependent diabetes, Faisalabad histiocytosis, and dysosteosclerosis. However, all these disorders with their different names and terminologies are actually the same entity termed H syndrome
Title: A novel homozygous frame-shift mutation in the SLC29A3 gene: a new case report and review of literature.

Submit: New GeneRIF Correction See all GeneRIFs (35)

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
H syndrome MedGen: C1864445 OMIM: 602782 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Association analyses identify three susceptibility Loci for vitiligo in the Chinese Han population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-148072 (e-PCR)
- UniSTS:176178

SHGC-149021 (e-PCR)
- UniSTS:176745

SHGC-147348 (e-PCR)
- UniSTS:175757

SHGC-146629 (e-PCR)
- UniSTS:175337

WI-17123 (e-PCR)
- UniSTS:79345

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cytidine transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables guanine transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables monoamine transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables neurotransmitter transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables nucleobase transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables nucleoside transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables nucleoside transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables nucleoside transmembrane transporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables nucleoside transmembrane transporter activity	TAS Traceable Author Statement more info
enables organic cation transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables uracil transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables uridine transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in adenosine transport	IDA Inferred from Direct Assay more info	PubMed
involved_in adenosine transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cytidine transport	IDA Inferred from Direct Assay more info	PubMed
involved_in dopamine transport	IDA Inferred from Direct Assay more info	PubMed
involved_in guanine transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in inosine transport	IDA Inferred from Direct Assay more info	PubMed
involved_in neurotransmitter transport	IEA Inferred from Electronic Annotation more info
involved_in norepinephrine transport	IDA Inferred from Direct Assay more info	PubMed
involved_in nucleobase transport	IDA Inferred from Direct Assay more info	PubMed
involved_in nucleoside transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in nucleoside transmembrane transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nucleoside transport	IDA Inferred from Direct Assay more info	PubMed
involved_in nucleoside transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in purine nucleobase transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in pyrimidine nucleobase transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in serotonin transport	IDA Inferred from Direct Assay more info	PubMed
involved_in uracil transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in uridine transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in xenobiotic metabolic process	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
is_active_in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in late endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	HDA more info	PubMed
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	TAS Traceable Author Statement more info
located_in mitochondrial outer membrane	TAS Traceable Author Statement more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: equilibrative nucleoside transporter 3

Names: solute carrier family 29 (equilibrative nucleoside transporter), member 3; solute carrier family 29 (nucleoside transporters), member 3

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

NG_017066.2 RefSeqGene

Range

5001..49127

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1318

mRNA and Protein(s)

NM_001174098.2 → NP_001167569.1 equilibrative nucleoside transporter 3 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. It encodes isoform b, which is shorter than isoform a.

Source sequence(s)

BC063019, BC120997, DC319920

UniProtKB/Swiss-Prot

Q9BZD2

Conserved Domains (1) summary

cl15430
Location:57 → 258

Nucleoside_tran; Nucleoside transporter
NM_001363518.2 → NP_001350447.1 equilibrative nucleoside transporter 3 isoform c

Status: REVIEWED

Source sequence(s)

AL359183, AL359384

Consensus CDS

CCDS86099.1

UniProtKB/TrEMBL

A0A2R8YDR8

Related

ENSP00000493995.1, ENST00000479577.2

Conserved Domains (1) summary

cl15430
Location:16 → 397

Nucleoside_tran; Nucleoside transporter
NM_018344.6 → NP_060814.4 equilibrative nucleoside transporter 3 isoform a

See identical proteins and their annotated locations for NP_060814.4

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a).

Source sequence(s)

BC050589, BC120997, DC319920

Consensus CDS

CCDS7310.1

UniProtKB/Swiss-Prot

B2RB50, B4E2Z9, B7ZA37, Q0VAM9, Q5T465, Q7RTT8, Q8IVZ0, Q9BWI2, Q9BZD2, Q9NUS9

Related

ENSP00000362285.5, ENST00000373189.6

Conserved Domains (1) summary

cl15430
Location:57 → 475

Nucleoside_tran; Nucleoside transporter

RNA

NR_033413.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

BC050589, BC120997, DC319920

Related

ENST00000644591.1
NR_033414.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

BC050589, BC120997, DC319920

Related

ENST00000644088.1

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

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

71319259..71381423

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047425425.1 → XP_047281381.1 equilibrative nucleoside transporter 3 isoform X2
XM_047425424.1 → XP_047281380.1 equilibrative nucleoside transporter 3 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060934.1 Alternate T2T-CHM13v2.0

Range

72188806..72250962

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054366210.1 → XP_054222185.1 equilibrative nucleoside transporter 3 isoform X2
XM_054366209.1 → XP_054222184.1 equilibrative nucleoside transporter 3 isoform X1