PITPNM1 phosphatidylinositol transfer protein membrane associated 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PITPNM1provided by HGNC
Official Full Name: phosphatidylinositol transfer protein membrane associated 1provided by HGNC
Primary source: HGNC:HGNC:9003
See related: Ensembl:ENSG00000110697 MIM:608794; AllianceGenome:HGNC:9003
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: Rd9; NIR2; RDGB; DRES9; RDGB1; RDGBA; PITPNM; RDGBA1
Summary: PITPNM1 belongs to a family of membrane-associated phosphatidylinositol transfer domain-containing proteins that share homology with the Drosophila retinal degeneration B (rdgB) protein (Ocaka et al., 2005 [PubMed 15627748]).[supplied by OMIM, Mar 2008]
Expression: Ubiquitous expression in spleen (RPKM 10.5), lymph node (RPKM 9.7) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q13.2

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (67491768..67506266, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (67485895..67500943, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (67259239..67272834, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Attenuation of PITPNM1 Signaling Cascade Can Inhibit Breast Cancer Progression.
Title: Attenuation of PITPNM1 Signaling Cascade Can Inhibit Breast Cancer Progression.
Authors found that the phosphatidylinositol transfer protein Nir2 acts as an LTP and may replenish PI at the HCV RO by interacting with VAMP-associated proteins (VAPs), enabling continuous viral replication during chronic infection.
Title: Nir2 Is an Effector of VAPs Necessary for Efficient Hepatitis C Virus Replication and Phosphatidylinositol 4-Phosphate Enrichment at the Viral Replication Organelle.
results suggest that Nir2 not only enhances EMT in vitro and breast cancer metastasis in animal models, but also contributes to breast cancer progression in human patients.
Title: The lipid-transfer protein Nir2 enhances epithelial-mesenchymal transition and facilitates breast cancer metastasis.
Phosphatidic acid production triggers Phosphatidylinositol 4,5-Bisphosphate replenishment mediated by Nir2 and Nir3 at endoplasmic reticulum-plasma membrane junctions.
Title: Phosphatidylinositol 4,5-Bisphosphate Homeostasis Regulated by Nir2 and Nir3 Proteins at Endoplasmic Reticulum-Plasma Membrane Junctions.
Nir2 translocates from the Golgi complex to the plasma membrane in response to GF stimulation.
Title: The phosphatidylinositol-transfer protein Nir2 binds phosphatidic acid and positively regulates phosphoinositide signalling.
Results suggest a feedback mechanism that replenishes PM PIP2 during receptor-induced Ca(2+) signaling via the Ca(2+) effector E-Syt1 and the PITP Nir2 at ER-PM junctions.
Title: Feedback regulation of receptor-induced Ca2+ signaling mediated by E-Syt1 and Nir2 at endoplasmic reticulum-plasma membrane junctions.
A specific Thr residue in the Nir2 PI-transfer domain provides a regulatory site for targeting to lipid droplets. This may affect intracellular lipid trafficking & distribution & explain the dominant effect of the RdgB-T59E mutant on retinal degeneration.
Title: Targeting of Nir2 to lipid droplets is regulated by a specific threonine residue within its PI-transfer domain.
Nir2 is involved in maintaining a critical DAG pool in the Golgi apparatus by regulating its consumption via the CDP-choline pathway
Title: Maintenance of the diacylglycerol level in the Golgi apparatus by the Nir2 protein is critical for Golgi secretory function.
Phosphorylation of Nir2 by Cdk1 facilitates its dissociation from the Golgi apparatus, and phospho-Nir2 is localized in the cleavage furrow and midbody during cytokinesis.
Title: Mitotic phosphorylation of the peripheral Golgi protein Nir2 by Cdk1 provides a docking mechanism for Plk1 and affects cytokinesis completion.
Nir2, a human homolog of Drosophila melanogaster retinal degeneration B protein, is essential for cytokinesis.
Title: Nir2, a human homolog of Drosophila melanogaster retinal degeneration B protein, is essential for cytokinesis.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

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

RH77932 (e-PCR)
- UniSTS:50216

WI-13814 (e-PCR)
- UniSTS:76379

WI-22393 (e-PCR)
- UniSTS:58002

MARC_14467-14468:1010602982:1 (e-PCR)
- UniSTS:267679

MARC_14467-14468:1027708983:1 (e-PCR)
- UniSTS:267679

SHGC-34148 (e-PCR)
- UniSTS:25796

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidic acid binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylcholine binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylcholine binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylcholine transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol transfer activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol transfer activity	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol transfer activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables receptor tyrosine kinase binding	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in brain development	TAS Traceable Author Statement more info	PubMed
involved_in intermembrane lipid transfer	IEA Inferred from Electronic Annotation more info
involved_in lipid metabolic process	NAS Non-traceable Author Statement more info	PubMed
involved_in phosphatidylinositol biosynthetic process	TAS Traceable Author Statement more info
involved_in phospholipid transport	IDA Inferred from Direct Assay more info	PubMed
involved_in phototransduction	TAS Traceable Author Statement more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi cisterna membrane	IEA Inferred from Electronic Annotation more info
located_in cell body	ISS Inferred from Sequence or Structural Similarity more info
located_in cleavage furrow	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in lipid droplet	IEA Inferred from Electronic Annotation more info
located_in membrane	TAS Traceable Author Statement more info	PubMed
located_in midbody	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: membrane-associated phosphatidylinositol transfer protein 1

Names: NIR-2; PITPnm 1; PYK2 N-terminal domain-interacting receptor 2; drosophila retinal degeneration B homolog; retinal degeneration B alpha 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.

mRNA and Protein(s)

NM_001130848.2 → NP_001124320.1 membrane-associated phosphatidylinositol transfer protein 1 isoform b

See identical proteins and their annotated locations for NP_001124320.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site at the end of an exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is 1 aa shorter compared to isoform a.

Source sequence(s)

AA465501, AK312886, BC022230, X98654

Consensus CDS

CCDS44659.1

UniProtKB/TrEMBL

B2R787

Related

ENSP00000398787.2, ENST00000436757.7

Conserved Domains (4) summary

cd08889
Location:1 → 257

SRPBCC_PITPNM1-2_like; Lipid-binding SRPBCC domain of mammalian PITPNM1-2 and related proteins (Class IIA PITPs)

smart00775
Location:1022 → 1153

LNS2; This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain and phosphatidylinositol transfer proteins

pfam02862
Location:689 → 878

DDHD; DDHD domain

cl21470
Location:963 → 1027

Peptidase_M14NE-CP-C_like; Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain
NM_004910.3 → NP_004901.2 membrane-associated phosphatidylinositol transfer protein 1 isoform a

See identical proteins and their annotated locations for NP_004901.2

Status: VALIDATED

Description

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

Source sequence(s)

AA465501, AF334584, AK312886, DA318858, X98654

Consensus CDS

CCDS31620.1

UniProtKB/Swiss-Prot

A6NME4, O00562, Q6T7X3, Q8TBN3, Q9BZ73

UniProtKB/TrEMBL

B2R787

Related

ENSP00000348772.3, ENST00000356404.8

Conserved Domains (4) summary

cd08889
Location:1 → 257

SRPBCC_PITPNM1-2_like; Lipid-binding SRPBCC domain of mammalian PITPNM1-2 and related proteins (Class IIA PITPs)

smart00775
Location:1023 → 1154

LNS2; This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain and phosphatidylinositol transfer proteins

pfam02862
Location:689 → 879

DDHD; DDHD domain

cl21470
Location:964 → 1028

Peptidase_M14NE-CP-C_like; Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction 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

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

67491768..67506266 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047427907.1 → XP_047283863.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X1

UniProtKB/Swiss-Prot

A6NME4, O00562, Q6T7X3, Q8TBN3, Q9BZ73
XM_047427911.1 → XP_047283867.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X4
XM_047427905.1 → XP_047283861.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X1

UniProtKB/Swiss-Prot

A6NME4, O00562, Q6T7X3, Q8TBN3, Q9BZ73
XM_047427909.1 → XP_047283865.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X2
XM_011545396.4 → XP_011543698.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X3

UniProtKB/TrEMBL

B2R787

Conserved Domains (4) summary

cd08889
Location:1 → 257

SRPBCC_PITPNM1-2_like; Lipid-binding SRPBCC domain of mammalian PITPNM1-2 and related proteins (Class IIA PITPs)

smart00775
Location:1022 → 1153

LNS2; This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain and phosphatidylinositol transfer proteins

pfam02862
Location:688 → 878

DDHD; DDHD domain

cl21470
Location:963 → 1027

Peptidase_M14NE-CP-C_like; Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain
XM_047427908.1 → XP_047283864.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X2
XM_017018586.2 → XP_016874075.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X1

UniProtKB/Swiss-Prot

A6NME4, O00562, Q6T7X3, Q8TBN3, Q9BZ73

UniProtKB/TrEMBL

B2R787

Conserved Domains (4) summary

cd08889
Location:1 → 257

SRPBCC_PITPNM1-2_like; Lipid-binding SRPBCC domain of mammalian PITPNM1-2 and related proteins (Class IIA PITPs)

smart00775
Location:1023 → 1154

LNS2; This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain and phosphatidylinositol transfer proteins

pfam02862
Location:689 → 879

DDHD; DDHD domain

cl21470
Location:964 → 1028

Peptidase_M14NE-CP-C_like; Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain
XM_047427910.1 → XP_047283866.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X2
XM_047427906.1 → XP_047283862.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X1

UniProtKB/Swiss-Prot

A6NME4, O00562, Q6T7X3, Q8TBN3, Q9BZ73

Related

ENSP00000437286.1, ENST00000534749.5
XM_047427913.1 → XP_047283869.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X6
XM_047427912.1 → XP_047283868.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X5
XM_047427915.1 → XP_047283871.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X8
XM_047427914.1 → XP_047283870.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X7
XM_047427916.1 → XP_047283872.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X9
XM_047427918.1 → XP_047283874.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X11
XM_047427917.1 → XP_047283873.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X10

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

67485895..67500943 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054370588.1 → XP_054226563.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X1

UniProtKB/Swiss-Prot

A6NME4, O00562, Q6T7X3, Q8TBN3, Q9BZ73
XM_054370594.1 → XP_054226569.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X4
XM_054370586.1 → XP_054226561.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X1

UniProtKB/Swiss-Prot

A6NME4, O00562, Q6T7X3, Q8TBN3, Q9BZ73
XM_054370591.1 → XP_054226566.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X2
XM_054370593.1 → XP_054226568.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X3
XM_054370590.1 → XP_054226565.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X2
XM_054370589.1 → XP_054226564.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X1

UniProtKB/Swiss-Prot

A6NME4, O00562, Q6T7X3, Q8TBN3, Q9BZ73
XM_054370592.1 → XP_054226567.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X2
XM_054370587.1 → XP_054226562.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X1

UniProtKB/Swiss-Prot

A6NME4, O00562, Q6T7X3, Q8TBN3, Q9BZ73
XM_054370596.1 → XP_054226571.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X6
XM_054370595.1 → XP_054226570.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X5
XM_054370598.1 → XP_054226573.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X8
XM_054370597.1 → XP_054226572.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X7
XM_054370599.1 → XP_054226574.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X9
XM_054370601.1 → XP_054226576.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X11
XM_054370600.1 → XP_054226575.1 membrane-associated phosphatidylinositol transfer protein 1 isoform X10