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ISYNA1 inositol-3-phosphate synthase 1 [ Homo sapiens (human) ]

Gene ID: 51477, updated on 2-Nov-2024

Summary

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Official Symbol
ISYNA1provided by HGNC
Official Full Name
inositol-3-phosphate synthase 1provided by HGNC
Primary source
HGNC:HGNC:29821
See related
Ensembl:ENSG00000105655 MIM:611670; AllianceGenome:HGNC:29821
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
IPS; INO1; INOS; IPS 1; IPS-1
Summary
This gene encodes an inositol-3-phosphate synthase enzyme. The encoded protein plays a critical role in the myo-inositol biosynthesis pathway by catalyzing the rate-limiting conversion of glucose 6-phosphate to myoinositol 1-phosphate. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 4. [provided by RefSeq, Nov 2011]
Expression
Broad expression in testis (RPKM 72.6), placenta (RPKM 57.0) and 14 other tissues See more
Orthologs
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Genomic context

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See ISYNA1 in Genome Data Viewer
Location:
19p13.11
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (18434388..18438133, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (18568567..18572312, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (18545198..18548943, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene microRNA 3189 Neighboring gene growth differentiation factor 15 Neighboring gene leucine rich repeat containing 25 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18518971-18519471 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10392 Neighboring gene CRISPRi-validated cis-regulatory element chr19.2899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18526865-18527500 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10393 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:18528379-18528618 Neighboring gene single stranded DNA binding protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10395 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18534153-18534654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18534655-18535154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18541209-18541757 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18541758-18542305 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10399 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18546343-18547240 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18548168-18549155 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18549156-18550142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18557131-18557659 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18561006-18561812 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18561813-18562619 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:18566359-18566575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14321 Neighboring gene elongation factor for RNA polymerase II Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18579531-18580168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10403 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18587281-18588108 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18589364-18590266 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:18594428-18594928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:18594929-18595429 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18596277-18596862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18605831-18606730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14323 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18611236-18612222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18618231-18619072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10405 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18631869-18632384 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18632385-18632900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18640318-18641203 Neighboring gene Sharpr-MPRA regulatory region 11651 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18652136-18652636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10407 Neighboring gene FKBP prolyl isomerase 8

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 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. [Clinicopathological significance of ISYNA1 expression in pancreatic ductal adenocarcinoma]. Zhou L, et al. Zhonghua Wai Ke Za Zhi, 2019 Mar 1. PMID 30861650
  2. L-myo-inositol-1-phosphate synthase expressed in developing organ: isolation and characterisation of the enzyme from human fetal liver. Chhetri DR, et al. Appl Biochem Biotechnol, 2012 Aug. PMID 22707096
  3. ISYNA1 is overexpressed in bladder carcinoma and regulates cell proliferation and apoptosis. Guo X, et al. Biochem Biophys Res Commun, 2019 Nov 5. PMID 31495492
  4. cDNA cloning and gene expression analysis of human myo-inositol 1-phosphate synthase. Guan G, et al. Arch Biochem Biophys, 2003 Sep 15. PMID 12941308
  5. E2F1 regulation of the human myo-inositol 1-phosphate synthase (ISYNA1) gene promoter. Seelan RS, et al. Arch Biochem Biophys, 2004 Nov 1. PMID 15464731

See all (55) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Cigarette smoke induces the ROS accumulation and iNOS activation through deactivation of Nrf-2/SIRT3 axis to mediate the human bronchial epithelium ferroptosis.
    Title: Cigarette smoke induces the ROS accumulation and iNOS activation through deactivation of Nrf-2/SIRT3 axis to mediate the human bronchial epithelium ferroptosis.
  2. The myo-inositol biosynthesis rate-limiting enzyme ISYNA1 suppresses the stemness of ovarian cancer via Notch1 pathway.
    Title: The myo-inositol biosynthesis rate-limiting enzyme ISYNA1 suppresses the stemness of ovarian cancer via Notch1 pathway.
  3. Musashi2 promotes the progression of pancreatic cancer through a novel ISYNA1-p21/ZEB-1 pathway.
    Title: Musashi2 promotes the progression of pancreatic cancer through a novel ISYNA1-p21/ZEB-1 pathway.
  4. The ISYNA1 was an important regulatory factors and related networks were involved in multiple functional processes.
    Title: ISYNA1 is overexpressed in bladder carcinoma and regulates cell proliferation and apoptosis.
  5. Abnormal expression of ISYNA1 may play an important role in the progression of pancreatic ductal adenocarcinoma
    Title: [Clinicopathological significance of ISYNA1 expression in pancreatic ductal adenocarcinoma].
  6. analysis of how myo-inositol-3-phosphate synthase is regulated by phosphorylation
    Title: Phosphorylation regulates myo-inositol-3-phosphate synthase: a novel regulatory mechanism of inositol biosynthesis.
  7. MIP synthase expressed in developing fetal liver and shows optima pH between 7.0 and 7.5.
    Title: L-myo-inositol-1-phosphate synthase expressed in developing organ: isolation and characterisation of the enzyme from human fetal liver.
  8. Upregulation occurs through the interaction of several low-affinity E2F binding motifs present in the minimal promoter.
    Title: E2F1 regulation of the human myo-inositol 1-phosphate synthase (ISYNA1) gene promoter.
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
An atlas of genetic influences on human blood metabolites.
EBI GWAS Catalog
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables inositol-3-phosphate synthase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables inositol-3-phosphate synthase activity IGI
Inferred from Genetic Interaction
more info
 PubMed 
enables inositol-3-phosphate synthase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in inositol biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in inositol biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in inositol biosynthetic process IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in phospholipid biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
inositol-3-phosphate synthase 1
Names
MI-1-P synthase
MIP synthase
myo-inositol 1-phosphate synthase A1
testis secretory sperm-binding protein Li 200a
NP_001164409.1
NP_001240318.1
NP_057452.1
XP_011526361.1
XP_054177164.1

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_031809.1 RefSeqGene

    Range
    5169..8914
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001170938.2 → NP_001164409.1  inositol-3-phosphate synthase 1 isoform 2

    See identical proteins and their annotated locations for NP_001164409.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AI983065, AK092179, BC018952, BP392170
    Consensus CDS
    CCDS54234.1
    UniProtKB/TrEMBL
    B3KSG0
    Related
    ENSP00000415458.3, ENST00000457269.8
    Conserved Domains (1) summary
    pfam07994
    Location:34 → 437
    NAD_binding_5; Myo-inositol-1-phosphate synthase

  2. NM_001253389.2 → NP_001240318.1  inositol-3-phosphate synthase 1 isoform 4

    See identical proteins and their annotated locations for NP_001240318.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AI983065, AL137749, BP392170
    Consensus CDS
    CCDS62603.1
    UniProtKB/TrEMBL
    B3KSG0
    Related
    ENSP00000475677.1, ENST00000578963.5
    Conserved Domains (1) summary
    pfam07994
    Location:1 → 363
    NAD_binding_5; Myo-inositol-1-phosphate synthase

  3. NM_016368.5 → NP_057452.1  inositol-3-phosphate synthase 1 isoform 1

    See identical proteins and their annotated locations for NP_057452.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AI983065, AK021526, BP392170
    Consensus CDS
    CCDS12379.1
    UniProtKB/Swiss-Prot
    B3KRT1, G5E9U0, Q6NXT5, Q7Z525, Q9BT65, Q9H2Y2, Q9NPH2, Q9NSU0, Q9NVW7
    UniProtKB/TrEMBL
    A0A140VK73
    Related
    ENSP00000337746.7, ENST00000338128.13
    Conserved Domains (1) summary
    cl00554
    Location:7 → 507
    NAD_binding_5; Myo-inositol-1-phosphate synthase

RNA

  1. NR_045573.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an internal exon 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)
    AI983065, AK296022, BP392170

  2. NR_045574.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks two exons in the 5' region, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI983065, AK093461, AL137749, BP392170, DA615868, DB244754
    Related
    ENST00000582811.6

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    18434388..18438133 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011528059.3 → XP_011526361.1  inositol-3-phosphate synthase 1 isoform X1

    Conserved Domains (1) summary
    cl00554
    Location:7 → 575
    NAD_binding_5; Myo-inositol-1-phosphate synthase

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    18568567..18572312 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054321189.1 → XP_054177164.1  inositol-3-phosphate synthase 1 isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001170939.1: Suppressed sequence

    Description
    NM_001170939.1: This RefSeq was permanently suppressed because currently there is insufficient support for the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NPH2.1 GenPept UniProtKB/Swiss-Prot:Q9NPH2

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