PITPNM2

phosphatidylinositol transfer protein membrane associated 2, the group of Phosphatidylinositol transfer proteins|MicroRNA protein coding host genes

Basic information

Region (hg38): 12:122983480-123151090

Links

ENSG00000090975 ∙ NCBI:57605 ∙ OMIM:608920 ∙ HGNC:21044 ∙ Uniprot:Q9BZ72 ∙ 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 PITPNM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PITPNM2 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			67	6		73
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	68	6	0

Variants in PITPNM2

This is a list of pathogenic ClinVar variants found in the PITPNM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-122986041-C-T		not specified	Likely benign (Mar 01, 2023)
12-122986047-C-T		not specified	Uncertain significance (May 15, 2024)
12-122986061-C-T		not specified	Uncertain significance (Dec 06, 2021)
12-122986062-G-A		not specified	Uncertain significance (May 31, 2022)
12-122986062-G-C		not specified	Uncertain significance (Sep 20, 2023)
12-122986102-C-T		not specified	Uncertain significance (Jul 30, 2023)
12-122986118-C-G		not specified	Uncertain significance (Feb 11, 2022)
12-122986157-C-T		not specified	Uncertain significance (Jul 13, 2021)
12-122986166-G-C		not specified	Uncertain significance (Jun 06, 2023)
12-122986208-C-T		not specified	Uncertain significance (Oct 12, 2022)
12-122986214-C-T		not specified	Uncertain significance (May 21, 2024)
12-122986233-C-T		not specified	Uncertain significance (Jul 26, 2022)
12-122986256-C-T		not specified	Uncertain significance (Nov 23, 2022)
12-122986268-C-T		not specified	Uncertain significance (Dec 09, 2023)
12-122986269-G-A		not specified	Uncertain significance (Dec 14, 2021)
12-122986283-C-T		not specified	Uncertain significance (Feb 23, 2023)
12-122986284-G-A		not specified	Uncertain significance (Dec 26, 2023)
12-122986295-G-A		not specified	Uncertain significance (Feb 15, 2023)
12-122986332-C-T		not specified	Uncertain significance (Jun 09, 2022)
12-122986679-G-C		not specified	Uncertain significance (Sep 22, 2023)
12-122986699-C-T		not specified	Uncertain significance (Oct 12, 2021)
12-122986723-C-T		not specified	Uncertain significance (Dec 18, 2023)
12-122987336-C-T		not specified	Uncertain significance (Dec 16, 2022)
12-122987342-C-T		not specified	Uncertain significance (Jan 06, 2023)
12-122987411-C-A		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PITPNM2	protein_coding	protein_coding	ENST00000320201	24	166536

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000216	125598	0	109	125707	0.000434

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.13	513	852	0.602	0.0000578	8743
Missense in Polyphen		254	511.67	0.49641		4998
Synonymous	1.65	338	379	0.892	0.0000282	2749
Loss of Function	6.48	5	58.5	0.0855	0.00000286	639

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00195	0.00193
Ashkenazi Jewish	0.000411	0.000397
East Asian	0.000272	0.000272
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000533	0.000528
Middle Eastern	0.000272	0.000272
South Asian	0.0000654	0.0000653
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transfer of phosphatidylinositol and phosphatidylcholine between membranes (in vitro). Binds calcium ions. {ECO:0000269|PubMed:10022914}.
• Pathway: Metabolism of lipids;Metabolism;Synthesis of PI;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.163
• rvis_EVS: -1.9
• rvis_percentile_EVS: 1.96

Haploinsufficiency Scores

• pHI: 0.158
• hipred: Y
• hipred_score: 0.662
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.732

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pitpnm2
• Phenotype: normal phenotype

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;phospholipid transport;phosphatidylinositol-mediated signaling
• Cellular component: cytoplasm;cytosol;endomembrane system;membrane;cell body
• Molecular function: calcium ion binding;phosphatidylcholine transporter activity;phosphatidylinositol transporter activity;receptor tyrosine kinase binding;phosphatidylcholine binding;phosphatidylinositol binding