PITPNC1

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

Basic information

Region (hg38): 17:67377281-67697256

Links

ENSG00000154217 ∙ NCBI:26207 ∙ OMIM:605134 ∙ HGNC:21045 ∙ Uniprot:Q9UKF7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PITPNC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PITPNC1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in PITPNC1

This is a list of pathogenic ClinVar variants found in the PITPNC1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-67532857-G-A		not specified	Uncertain significance (Jul 10, 2024)
17-67532877-G-A		not specified	Uncertain significance (Aug 04, 2024)
17-67532908-A-G		not specified	Uncertain significance (Mar 31, 2024)
17-67552268-G-C		not specified	Uncertain significance (Sep 10, 2024)
17-67552303-G-A		not specified	Uncertain significance (Aug 04, 2023)
17-67632203-G-A		not specified	Uncertain significance (Dec 18, 2023)
17-67669554-G-C		not specified	Uncertain significance (Apr 25, 2022)
17-67675536-T-G		not specified	Uncertain significance (May 05, 2023)
17-67675537-G-T		not specified	Uncertain significance (May 05, 2023)
17-67692575-T-C		not specified	Uncertain significance (Oct 17, 2024)
17-67692604-C-G		not specified	Uncertain significance (Oct 02, 2023)
17-67692637-G-A		not specified	Uncertain significance (Jun 10, 2022)
17-67692665-C-T		not specified	Uncertain significance (Dec 03, 2024)
17-67692695-G-A		not specified	Uncertain significance (Oct 06, 2021)
17-67692697-A-G		not specified	Uncertain significance (Nov 09, 2023)
17-67692757-G-A		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PITPNC1	protein_coding	protein_coding	ENST00000581322	9	319798

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00747	124631	0	6	124637	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.36	96	187	0.514	0.0000104	2171
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.0000493	0.0000464
European (Non-Finnish)	0.0000266	0.0000265
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.627
• hipred: Y
• hipred_score: 0.626
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.906

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pitpnc1

Zebrafish Information Network

• Gene name: pitpnc1a
• Affected structure: musculoskeletal movement
• Phenotype tag: abnormal
• Phenotype quality: increased occurrence

Gene ontology

• Biological process: signal transduction;phospholipid transport
• Cellular component: nucleoplasm;cytoplasm;cytosol
• Molecular function: protein binding;phosphatidylcholine transporter activity;phosphatidylinositol transporter activity;phosphatidylinositol binding;phosphatidic acid binding;phosphatidylglycerol binding