PITPNA

phosphatidylinositol transfer protein alpha, the group of Phosphatidylinositol transfer proteins

Basic information

Region (hg38): 17:1517718-1562792

Previous symbols: [ "PITPN" ]

Links

ENSG00000174238 ∙ NCBI:5306 ∙ OMIM:600174 ∙ HGNC:9001 ∙ Uniprot:Q00169 ∙ 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 PITPNA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PITPNA 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			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	1	0

Variants in PITPNA

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

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

Position	Type	Phenotype	Significance	ClinVar
17-1534133-C-T		not specified	Uncertain significance (Feb 27, 2023)
17-1534170-C-G		not specified	Uncertain significance (Sep 02, 2024)
17-1535216-C-A		not specified	Uncertain significance (Dec 03, 2021)
17-1535261-T-C		not specified	Uncertain significance (Feb 15, 2023)
17-1535280-T-A		not specified	Uncertain significance (Dec 13, 2023)
17-1535497-G-T		not specified	Uncertain significance (Nov 24, 2024)
17-1538889-G-C		not specified	Uncertain significance (Dec 20, 2023)
17-1538910-C-T		not specified	Likely benign (Apr 25, 2023)
17-1538926-C-G		not specified	Uncertain significance (Nov 13, 2024)
17-1541576-G-A		not specified	Uncertain significance (Jun 10, 2024)
17-1548307-T-C		not specified	Uncertain significance (Nov 26, 2024)
17-1553034-T-C		not specified	Uncertain significance (May 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PITPNA	protein_coding	protein_coding	ENST00000313486	11	45099

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.965	0.0349	124631	0	7	124638	0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	67	152	0.442	0.00000831	1791
Missense in Polyphen		25	61.966	0.40345		757
Synonymous	-0.180	61	59.2	1.03	0.00000395	466
Loss of Function	3.94	3	23.7	0.127	0.00000136	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000870	0.0000870
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transfer of PtdIns and phosphatidylcholine between membranes.
• Pathway: Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;Developmental Biology;Role of second messengers in netrin-1 signaling;EGFR1;Netrin-1 signaling;Axon guidance;Netrin-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.550
• hipred: Y
• hipred_score: 0.775
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.718

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pitpna
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: pitpnaa
• Affected structure: CaP motoneuron
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: lipid metabolic process;axonogenesis;visual perception;phospholipid transport;interleukin-12-mediated signaling pathway
• Cellular component: cytoplasm;cytosol;myelin sheath;extracellular exosome
• Molecular function: phosphatidylcholine transporter activity;phosphatidylinositol transporter activity;phosphatidylcholine binding;phosphatidylinositol binding;phosphatidylglycerol binding