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NT5DC1 5'-nucleotidase domain containing 1 [ Homo sapiens (human) ]

Gene ID: 221294, updated on 5-Mar-2024

Summary

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Official Symbol
NT5DC1provided by HGNC
Official Full Name
5'-nucleotidase domain containing 1provided by HGNC
Primary source
HGNC:HGNC:21556
See related
Ensembl:ENSG00000178425 AllianceGenome:HGNC:21556
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
LP2642; NT5C2L1; C6orf200
Summary
While the exact function of the protein encoded by this gene is not known, it belongs to the 5'(3')-deoxyribonucleotidase family. [provided by RefSeq, May 2010]
Expression
Ubiquitous expression in thyroid (RPKM 16.7), prostate (RPKM 14.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
6q22.1
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (116100853..116249497)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (117284838..117433477)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (116422016..116570660)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901385 Neighboring gene NANOG hESC enhancer GRCh37_chr6:116235207-116235708 Neighboring gene fyn related Src family tyrosine kinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24976 Neighboring gene triosephosphate isomerase 1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24978 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24979 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:116412309-116412554 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:116421676-116422198 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:116422199-116422719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24980 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88050 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88070 Neighboring gene Sharpr-MPRA regulatory region 2872 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88113 Neighboring gene MPRA-validated peak6050 silencer Neighboring gene collagen type X alpha 1 chain Neighboring gene NIP7 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24981 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24982 Neighboring gene ribosomal protein S5 pseudogene Neighboring gene TSPY like 4 Neighboring gene RPS5 pseudogene 1 Neighboring gene dermatan sulfate epimerase

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. Single-nucleotide polymorphisms in the TSPYL-4 and NT5DC1 genes are associated with susceptibility to chronic obstructive pulmonary disease. Guo Y, et al. Mol Med Rep, 2012 Sep. PMID 22736055
  2. Weighted gene co-expression network analysis identifies specific modules and hub genes related to subsyndromal symptomatic depression. Geng R, et al. World J Biol Psychiatry, 2020 Feb. PMID 30489189
  3. Seven new loci associated with age-related macular degeneration. Fritsche LG, et al. Nat Genet, 2013 Apr. PMID 23455636, Free PMC Article
  4. GWAS of dental caries patterns in the permanent dentition. Shaffer JR, et al. J Dent Res, 2013 Jan. PMID 23064961, Free PMC Article
  5. Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts. Vieira AR, et al. Genet Med, 2008 Sep. PMID 18978678, Free PMC Article

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Weighted gene co-expression network analysis identifies specific modules and hub genes related to subsyndromal symptomatic depression.
    Title: Weighted gene co-expression network analysis identifies specific modules and hub genes related to subsyndromal symptomatic depression.
  2. The rs1052443 C allele of NT5DC1 was associated with a protective effect against the deterioration of pulmonary function.
    Title: Single-nucleotide polymorphisms in the TSPYL-4 and NT5DC1 genes are associated with susceptibility to chronic obstructive pulmonary disease.
  3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
GWAS of dental caries patterns in the permanent dentition.
EBI GWAS Catalog
Seven new loci associated with age-related macular degeneration.
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)

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

  • MGC24302, MGC131837

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 5'-nucleotidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
5'-nucleotidase domain-containing protein 1
Names
5'-nucleotidase, cytosolic II-like 1 protein

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_021351.2 RefSeqGene

    Range
    5002..153646
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_152729.3 → NP_689942.2  5'-nucleotidase domain-containing protein 1

    See identical proteins and their annotated locations for NP_689942.2

    Status: REVIEWED

    Source sequence(s)
    AL050331, AL121963, KF458258
    Consensus CDS
    CCDS5104.1
    UniProtKB/Swiss-Prot
    B2RND9, B3KR35, Q5TFE4, Q6XYD5
    UniProtKB/TrEMBL
    A8K2Z3
    Related
    ENSP00000326858.3, ENST00000319550.9
    Conserved Domains (1) summary
    cl17687
    Location:11 → 337
    5_nucleotid; 5' nucleotidase family

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    116100853..116249497
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006715378.4 → XP_006715441.1  5'-nucleotidase domain-containing protein 1 isoform X1

    Conserved Domains (1) summary
    cl17687
    Location:11 → 299
    5_nucleotid; 5' nucleotidase family

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    117284838..117433477
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054354520.1 → XP_054210495.1  5'-nucleotidase domain-containing protein 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5TFE4.1 GenPept UniProtKB/Swiss-Prot:Q5TFE4

Gene LinkOut

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