PITPNC1

protein-coding

phosphatidylinositol transfer protein cytoplasmic 1, the group of MicroRNA protein coding host genes|Phosphatidylinositol transfer proteins

Gene summary

This gene encodes a member of the phosphatidylinositol transfer protein family. The encoded cytoplasmic protein plays a role in multiple processes including cell signaling and lipid metabolism by facilitating the transfer of phosphatidylinositol between membrane compartments. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 1. [provided by RefSeq, May 2012]

MANE transcript

NM_012417.4

Inheritance

—

ClinVar variants

U:29

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr17:67,377,281-67,697,256

External References & Databases

Ensembl (ENSG00000154217)

Transcript & Mutation Effects

hg38 • Region Span ~320.0 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 PITPNC1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 24

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012417.4. 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			1 clinvar			1
missense			26 clinvar			26
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	29	0	0	29

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012417.4	RefSeq	NP_036549.2	9	MANE Select
ENST00000581322.6	Ensembl	ENSP00000464006.1	9	MANE Select
NM_181671.3	RefSeq	NP_858057.1	10	Standard
ENST00000580974.6	Ensembl	ENSP00000463626.1	10	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
pitpnc1a	Danio rerio	Structure: musculoskeletal movement Quality: increased occurrence abnormal

Gene / Model

Organism

Observed Phenotype

pitpnc1a

Danio rerio

Structure: musculoskeletal movement

Quality: increased occurrence

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

signal transduction
phospholipid transport

Molecular Function

protein binding
phosphatidylcholine transporter activity
phosphatidylinositol transporter activity
phosphatidylinositol binding
phosphatidic acid binding

Cellular Component

nucleoplasm
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000581322
Coding exons: 9
Length: 319798
Individuals with no LoFs: 124631
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 124637
p: 0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.36	96	187	0.514	0.0000104	2171
Missense (PolyPhen)		22	67.865	0.32417		797
Synonymous	0.499	64	69.3	0.924	0.00000401	619
Loss of Function	3.83	1	19.0	0.0525	0.00000106	220

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0.000049	0.000046	rare
European (Non-Finnish)	0.000027	0.000027	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Phosphatidylinositol transfer proteins mediate the monomeric transport of lipids by shielding a lipid from the aqueous environment and binding the lipid in a hydrophobic cavity. Able to transfer phosphatidylinositol in vitro. {ECO:0000269|PubMed:10531358}.;

Recessive Scores

pRec: 0.0960

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.906

Gene Damage Prediction

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