PITPNM2

protein-coding

phosphatidylinositol transfer protein membrane associated 2, the group of Phosphatidylinositol transfer proteins|MicroRNA protein coding host genes

Gene 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]

MANE transcript

NM_020845.3

Inheritance

—

ClinVar variants

U:179B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr12:122,983,480-123,151,090

External References & Databases

Ensembl (ENSG00000090975)

Transcript & Mutation Effects

hg38 • Region Span ~167.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PITPNM2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 177

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020845.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	2 clinvar		6
missense			169 clinvar	12 clinvar		181
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	179	14	0	193

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 51 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020845.3	RefSeq	NP_065896.1	24	MANE Select
ENST00000320201.10	Ensembl	ENSP00000322218.4	24	MANE Select
NM_001300801.2	RefSeq	NP_001287730.1	24	Standard
NM_001384660.1	RefSeq	NP_001371589.1	25	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of lipids
Metabolism
Synthesis of PI
Glycerophospholipid biosynthesis
Phospholipid metabolism

Biological Process

phosphatidylinositol biosynthetic process
phospholipid transport
phosphatidylinositol-mediated signaling

Molecular Function

calcium ion binding
phosphatidylcholine transporter activity
phosphatidylinositol transporter activity
receptor tyrosine kinase binding
phosphatidylcholine binding

Cellular Component

cytoplasm
cytosol
endomembrane system
membrane
cell body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000320201
Coding exons: 24
Length: 166536
Individuals with no LoFs: 125598
Homozygous LoFs: 0
Heterozygous LoFs: 109
Defined: 125707
p: 0.000434

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	4.13	513	852	0.602	0.0000578	8743
Missense (PolyPhen)		254	511.67	0.49641		4998
Synonymous	1.65	338	379	0.892	0.0000282	2749
Loss of Function	6.48	5	58.5	0.0855	0.00000286	639

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0019	0.0018	notable
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.00041	0.00040	rare
East Asian	0.00027	0.00027	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00053	0.00053	rare
South Asian	0.000065	0.000065	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the transfer of phosphatidylinositol and phosphatidylcholine between membranes (in vitro). Binds calcium ions. {ECO:0000269|PubMed:10022914}.;

Recessive Scores

pRec: 0.120

Intolerance Scores

LoFtool: 0.163
RVIS EVS: -1.9
RVIS percentile EVS: 1.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.732

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium