PITPNB

phosphatidylinositol transfer protein beta, the group of Phosphatidylinositol transfer proteins

Basic information

Region (hg38): 22:27851669-27920134

Links

ENSG00000180957 ∙ NCBI:23760 ∙ OMIM:606876 ∙ HGNC:9002 ∙ Uniprot:P48739 ∙ 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 PITPNB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PITPNB 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			6			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	6	0	0

Variants in PITPNB

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

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

Position	Type	Phenotype	Significance	ClinVar
22-27854911-G-A		not specified	Uncertain significance (Dec 21, 2022)
22-27873797-C-A		not specified	Uncertain significance (Feb 21, 2025)
22-27897821-G-A		not specified	Uncertain significance (Jan 22, 2024)
22-27897838-A-C		not specified	Uncertain significance (Oct 09, 2024)
22-27897878-A-G		not specified	Uncertain significance (Aug 15, 2024)
22-27910988-G-A		not specified	Uncertain significance (Aug 08, 2022)
22-27911012-T-G		not specified	Uncertain significance (Mar 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PITPNB	protein_coding	protein_coding	ENST00000335272	11	68466

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.981	0.0190	125736	0	2	125738	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.15	49	114	0.431	0.00000548	1807
Missense in Polyphen		11	51.622	0.21309		800
Synonymous	0.603	35	39.8	0.879	0.00000212	458
Loss of Function	3.54	1	16.5	0.0606	6.95e-7	251

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transfer of PtdIns and phosphatidylcholine between membranes.
• Pathway: Metabolism of lipids;Metabolism;PI and PC transport between ER and Golgi membranes;PI Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.199
• rvis_EVS: 0.12
• rvis_percentile_EVS: 62.38

Haploinsufficiency Scores

• pHI: 0.320
• hipred: Y
• hipred_score: 0.728
• ghis: 0.621

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.575

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pitpnb
• Phenotype: 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)

Zebrafish Information Network

• Gene name: pitpnb
• Affected structure: retinal cone cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: lipid metabolic process;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;nucleus organization;phospholipid transport
• Cellular component: Golgi membrane;cytoplasm;endoplasmic reticulum membrane
• Molecular function: phosphatidylcholine transporter activity;phosphatidylinositol transporter activity;phosphatidylcholine binding;phosphatidylinositol binding