PITPNM1

protein-coding

phosphatidylinositol transfer protein membrane associated 1, the group of Phosphatidylinositol transfer proteins

Gene 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]

Previous symbols:

PITPNM

MANE transcript

NM_004910.3

Inheritance

—

ClinVar variants

U:183B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr11:67,491,760-67,506,263

External References & Databases

Ensembl (ENSG00000110697)

Transcript & Mutation Effects

hg38 • Region Span ~14.5 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 PITPNM1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 175

not providedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004910.3. 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			3 clinvar	5 clinvar	1 clinvar	9
missense			175 clinvar	3 clinvar	2 clinvar	180
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	183	8	3	194

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004910.3	RefSeq	NP_004901.2	23	MANE Select
ENST00000356404.8	Ensembl	ENSP00000348772.3	23	MANE Select
NM_001130848.2	RefSeq	NP_001124320.1	23	Standard
ENST00000436757.6	Ensembl	ENSP00000398787.2	23	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

lipid metabolic process
phosphatidylinositol biosynthetic process
brain development
phototransduction
protein transport

Molecular Function

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

Cellular Component

cytoplasm
endoplasmic reticulum membrane
lipid droplet
microtubule organizing center
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000356404
Coding exons: 23
Length: 14496
Individuals with no LoFs: 125575
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 125608
p: 0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.19	565	822	0.687	0.0000569	7941
Missense (PolyPhen)		126	260.3	0.48406		2567
Synonymous	-0.556	379	365	1.04	0.0000278	2619
Loss of Function	5.06	17	58.9	0.289	0.00000303	618

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.00013	0.00012	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000099	0.000092	rare
European (Non-Finnish)	0.00016	0.00015	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Regulates RHOA activity, and plays a role in cytoskeleton remodeling. Necessary for normal completion of cytokinesis. Plays a role in maintaining normal diacylglycerol levels in the Golgi apparatus. Binds phosphatidyl inositol phosphates (in vitro). May catalyze the transfer of phosphatidylinositol and phosphatidylcholine between membranes (By similarity). Necessary for maintaining the normal structure of the endoplasmic reticulum and the Golgi apparatus. Required for protein export from the endoplasmic reticulum and the Golgi. Binds calcium ions. {ECO:0000250, ECO:0000269|PubMed:10022914, ECO:0000269|PubMed:11909959, ECO:0000269|PubMed:15545272, ECO:0000269|PubMed:15723057}.;

Recessive Scores

pRec: 0.150

Intolerance Scores

LoFtool: 0.473
RVIS EVS: -1.01
RVIS percentile EVS: 8.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.805

Gene Damage Prediction

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