PITPNM2 phosphatidylinositol transfer protein membrane associated 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PITPNM2provided by HGNC
Official Full Name: phosphatidylinositol transfer protein membrane associated 2provided by HGNC
Primary source: HGNC:HGNC:21044
See related: Ensembl:ENSG00000090975 MIM:608920; AllianceGenome:HGNC:21044
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: NIR3; NIR-3; RDGB2; RDGBA2
Summary: PITPNM2 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 ovary (RPKM 9.1), brain (RPKM 5.5) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q24.31

Exon count:: 33

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (122983480..123151848, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (122980005..123147639, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (123468027..123635637, complement)

Chromosome 12 - NC_000012.12 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
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?

PITPNM2 was associated with bipolar disorder.
Title: Whole-exome sequencing of individuals from an isolated population implicates rare risk variants in bipolar disorder.

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
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method. EBI GWAS Catalog EBI GWAS CatalogPubMed
Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis identifies 13 new risk loci for schizophrenia. 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

GC18S01 (e-PCR)
- UniSTS:464643

D12S2067 (e-PCR)
- UniSTS:8036

SHGC-156254 (e-PCR)
- UniSTS:182630

RH123438 (e-PCR)
- UniSTS:135826

SHGC-144564 (e-PCR)
- UniSTS:172281

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylcholine binding	IBA Inferred from Biological aspect of Ancestor more info
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 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 intermembrane lipid transfer	IEA Inferred from Electronic Annotation more info
involved_in phosphatidylinositol biosynthetic process	TAS Traceable Author Statement more info
involved_in phospholipid transport	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
located_in endomembrane system	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: membrane-associated phosphatidylinositol transfer protein 2

Names: PYK2 N-terminal domain-interacting receptor 3; retinal degeneration B alpha 2

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_001300801.2 → NP_001287730.1 membrane-associated phosphatidylinositol transfer protein 2 isoform 2

See identical proteins and their annotated locations for NP_001287730.1

Status: VALIDATED

Source sequence(s)

AC026362, AC073857

Consensus CDS

CCDS73543.1

UniProtKB/Swiss-Prot

Q9BZ72

Conserved Domains (3) summary

cd08889
Location:1 → 258

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

smart00775
Location:1102 → 1233

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

pfam02862
Location:718 → 956

DDHD; DDHD domain
NM_001384660.1 → NP_001371589.1 membrane-associated phosphatidylinositol transfer protein 2 isoform 3

Status: VALIDATED

Source sequence(s)

AC026362, AC073857

Conserved Domains (4) summary

cd08889
Location:1 → 258

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

COG5083
Location:1101 → 1240

SMP2; Phosphatidate phosphatase PAH1, contains Lipin and LNS2 domains. can be involved in plasmid maintenance [Lipid transport and metabolism]

pfam02862
Location:718 → 1048

DDHD; DDHD domain

cl21460
Location:1194 → 1292

HAD_like; Haloacid Dehalogenase-like Hydrolases
NM_001384661.1 → NP_001371590.1 membrane-associated phosphatidylinositol transfer protein 2 isoform 4

Status: VALIDATED

Source sequence(s)

AC026362, AC073857

Conserved Domains (3) summary

cd08889
Location:1 → 258

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

smart00775
Location:1054 → 1185

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

pfam02862
Location:718 → 908

DDHD; DDHD domain
NM_001384662.1 → NP_001371591.1 membrane-associated phosphatidylinositol transfer protein 2 isoform 6

Status: VALIDATED

Source sequence(s)

AC026362, AC073857

Conserved Domains (3) summary

cd08889
Location:1 → 258

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

smart00775
Location:1051 → 1182

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

pfam02862
Location:718 → 905

DDHD; DDHD domain
NM_001384663.1 → NP_001371592.1 membrane-associated phosphatidylinositol transfer protein 2 isoform 4

Status: VALIDATED

Source sequence(s)

AC026362, AC073857

Conserved Domains (3) summary

cd08889
Location:1 → 258

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

smart00775
Location:1054 → 1185

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

pfam02862
Location:718 → 908

DDHD; DDHD domain
NM_001384664.1 → NP_001371593.1 membrane-associated phosphatidylinositol transfer protein 2 isoform 7

Status: VALIDATED

Source sequence(s)

AC026362, AC073857

Conserved Domains (3) summary

cd08889
Location:1 → 258

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

smart00775
Location:1037 → 1168

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

pfam02862
Location:701 → 891

DDHD; DDHD domain
NM_001384665.1 → NP_001371594.1 membrane-associated phosphatidylinositol transfer protein 2 isoform 8

Status: VALIDATED

Source sequence(s)

AC026362, AC073857

UniProtKB/TrEMBL

A5D8U3, S4R414

Related

ENST00000451868.2

Conserved Domains (1) summary

cd08889
Location:1 → 258

SRPBCC_PITPNM1-2_like; Lipid-binding SRPBCC domain of mammalian PITPNM1-2 and related proteins (Class IIA PITPs)
NM_001384666.1 → NP_001371595.1 membrane-associated phosphatidylinositol transfer protein 2 isoform 8

Status: VALIDATED

Source sequence(s)

AC026362, AC073857

UniProtKB/TrEMBL

A5D8U3, S4R414

Conserved Domains (1) summary

cd08889
Location:1 → 258

SRPBCC_PITPNM1-2_like; Lipid-binding SRPBCC domain of mammalian PITPNM1-2 and related proteins (Class IIA PITPs)
NM_001384667.1 → NP_001371596.1 membrane-associated phosphatidylinositol transfer protein 2 isoform 8

Status: VALIDATED

Source sequence(s)

AC026362, AC073857

UniProtKB/TrEMBL

A5D8U3, S4R414

Conserved Domains (1) summary

cd08889
Location:1 → 258

SRPBCC_PITPNM1-2_like; Lipid-binding SRPBCC domain of mammalian PITPNM1-2 and related proteins (Class IIA PITPs)
NM_001384668.1 → NP_001371597.1 membrane-associated phosphatidylinositol transfer protein 2 isoform 2

Status: VALIDATED

Source sequence(s)

AC026362, AC073857

Consensus CDS

CCDS73543.1

Conserved Domains (3) summary

cd08889
Location:1 → 258

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

smart00775
Location:1102 → 1233

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

pfam02862
Location:718 → 956

DDHD; DDHD domain
NM_020845.3 → NP_065896.1 membrane-associated phosphatidylinositol transfer protein 2 isoform 1

See identical proteins and their annotated locations for NP_065896.1

Status: VALIDATED

Source sequence(s)

AC026362, AC073857

Consensus CDS

CCDS9242.1

UniProtKB/Swiss-Prot

Q9BZ72, Q9P271

Related

ENSP00000322218.4, ENST00000320201.10

Conserved Domains (3) summary

cd08889
Location:1 → 258

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

smart00775
Location:1108 → 1239

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

pfam02862
Location:718 → 962

DDHD; DDHD domain

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

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

122983480..123151848 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047429206.1 → XP_047285162.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X7

UniProtKB/Swiss-Prot

Q9BZ72, Q9P271
XM_047429208.1 → XP_047285164.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X9

Related

ENSP00000280562.5, ENST00000280562.9
XM_047429215.1 → XP_047285171.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X15
XM_047429211.1 → XP_047285167.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X12
XM_047429204.1 → XP_047285160.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X4
XM_047429209.1 → XP_047285165.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X10
XM_047429203.1 → XP_047285159.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X3
XM_047429212.1 → XP_047285168.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X13
XM_047429205.1 → XP_047285161.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X6
XM_047429207.1 → XP_047285163.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X8
XM_047429202.1 → XP_047285158.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X2
XM_047429216.1 → XP_047285172.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X16
XM_047429210.1 → XP_047285166.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X11
XM_047429200.1 → XP_047285156.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X1
XM_047429213.1 → XP_047285169.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X14
XM_047429201.1 → XP_047285157.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X1
XM_047429214.1 → XP_047285170.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X14
XM_024449099.2 → XP_024304867.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X1

Conserved Domains (3) summary

cd08889
Location:1 → 258

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

smart00775
Location:1194 → 1325

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

pfam02862
Location:718 → 1048

DDHD; DDHD domain
XM_047429217.1 → XP_047285173.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X17
XM_024449100.2 → XP_024304868.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X5

Conserved Domains (3) summary

smart00775
Location:1128 → 1259

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

pfam02862
Location:652 → 982

DDHD; DDHD domain

cl14643
Location:1 → 192

SRPBCC; START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily
XM_024449101.2 → XP_024304869.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X18

UniProtKB/TrEMBL

Q9UF51

Conserved Domains (2) summary

smart00775
Location:810 → 941

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

pfam02862
Location:334 → 664

DDHD; DDHD domain

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

122980005..123147639 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054372666.1 → XP_054228641.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X16
XM_054372660.1 → XP_054228635.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X11
XM_054372649.1 → XP_054228624.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X1
XM_054372663.1 → XP_054228638.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X14
XM_054372651.1 → XP_054228626.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X1
XM_054372652.1 → XP_054228627.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X19
XM_054372665.1 → XP_054228640.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X15
XM_054372661.1 → XP_054228636.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X12
XM_054372655.1 → XP_054228630.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X4
XM_054372659.1 → XP_054228634.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X10
XM_054372654.1 → XP_054228629.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X3
XM_054372662.1 → XP_054228637.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X13
XM_054372657.1 → XP_054228632.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X6
XM_054372658.1 → XP_054228633.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X8
XM_054372653.1 → XP_054228628.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X2
XM_054372664.1 → XP_054228639.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X14
XM_054372650.1 → XP_054228625.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X1
XM_054372667.1 → XP_054228642.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X17
XM_054372656.1 → XP_054228631.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X5
XM_054372668.1 → XP_054228643.1 membrane-associated phosphatidylinositol transfer protein 2 isoform X18