PITPNM1

phosphatidylinositol transfer protein membrane associated 1, the group of Phosphatidylinositol transfer proteins

Basic information

Region (hg38): 11:67491767-67506263

Previous symbols: [ "PITPNM" ]

Links

ENSG00000110697 ∙ NCBI:9600 ∙ OMIM:608794 ∙ HGNC:9003 ∙ Uniprot:O00562 ∙ 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 PITPNM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PITPNM1 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				5	1	6
missense			74	2	2	78
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	74	7	3

Variants in PITPNM1

This is a list of pathogenic ClinVar variants found in the PITPNM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-67492039-C-G		not specified	Uncertain significance (May 26, 2023)
11-67492052-T-G		not specified	Uncertain significance (Apr 29, 2024)
11-67492088-G-T		not specified	Uncertain significance (Jun 18, 2021)
11-67492089-T-C		not specified	Uncertain significance (May 07, 2024)
11-67492138-C-T			Likely benign (Jun 10, 2018)
11-67492148-A-G		not specified	Uncertain significance (Oct 06, 2021)
11-67492151-T-C		not specified	Uncertain significance (Jun 11, 2021)
11-67492163-C-T		not specified	Uncertain significance (Jul 26, 2022)
11-67492209-A-G			Likely benign (Apr 05, 2018)
11-67492228-C-T			Likely benign (Feb 01, 2023)
11-67492250-C-G		not specified	Uncertain significance (Apr 12, 2022)
11-67492254-C-T		not specified	Uncertain significance (Jan 10, 2022)
11-67492275-C-A		not specified	Uncertain significance (Dec 26, 2023)
11-67493510-G-A		not specified	Uncertain significance (Mar 07, 2023)
11-67493769-C-G		not specified	Uncertain significance (May 30, 2024)
11-67493962-C-T		not specified	Uncertain significance (Nov 08, 2021)
11-67493963-G-T			Likely benign (Jan 01, 2023)
11-67493965-G-A		not specified	Uncertain significance (Apr 22, 2024)
11-67493974-G-C		not specified	Uncertain significance (Dec 28, 2022)
11-67494012-T-C		not specified	Uncertain significance (Dec 06, 2021)
11-67494064-C-T		not specified	Uncertain significance (Jul 05, 2023)
11-67494348-T-A		not specified	Uncertain significance (Mar 31, 2024)
11-67494850-A-G		not specified	Uncertain significance (Nov 16, 2022)
11-67494931-A-C		not specified	Uncertain significance (Aug 17, 2022)
11-67494940-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PITPNM1	protein_coding	protein_coding	ENST00000356404	23	14496

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00138	0.999	125575	0	33	125608	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.19	565	822	0.687	0.0000569	7941
Missense in Polyphen		126	260.3	0.48406		2567
Synonymous	-0.556	379	365	1.04	0.0000278	2619
Loss of Function	5.06	17	58.9	0.289	0.00000303	618

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000193	0.000192
Ashkenazi Jewish	0.000114	0.0000993
East Asian	0.000219	0.000217
Finnish	0.0000993	0.0000924
European (Non-Finnish)	0.000155	0.000150
Middle Eastern	0.000219	0.000217
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates RHOA activity, and plays a role in cytoskeleton remodeling. Necessary for normal completion of cytokinesis. Plays a role in maintaining normal diacylglycerol levels in the Golgi apparatus. Binds phosphatidyl inositol phosphates (in vitro). May catalyze the transfer of phosphatidylinositol and phosphatidylcholine between membranes (By similarity). Necessary for maintaining the normal structure of the endoplasmic reticulum and the Golgi apparatus. Required for protein export from the endoplasmic reticulum and the Golgi. Binds calcium ions. {ECO:0000250, ECO:0000269|PubMed:10022914, ECO:0000269|PubMed:11909959, ECO:0000269|PubMed:15545272, ECO:0000269|PubMed:15723057}.
• Pathway: Metabolism of lipids;Metabolism;Synthesis of PI;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.150

Intolerance Scores

• loftool: 0.473
• rvis_EVS: -1.01
• rvis_percentile_EVS: 8.2

Haploinsufficiency Scores

• pHI: 0.129
• hipred: Y
• hipred_score: 0.756
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.805

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pitpnm1
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; hearing/vestibular/ear phenotype; immune system phenotype

Gene ontology

• Biological process: lipid metabolic process;phosphatidylinositol biosynthetic process;brain development;phototransduction;protein transport;phospholipid transport
• Cellular component: cytoplasm;endoplasmic reticulum membrane;lipid droplet;microtubule organizing center;cytosol;membrane;midbody;cleavage furrow;Golgi cisterna membrane;cytoplasmic ribonucleoprotein granule;cell body
• Molecular function: calcium ion binding;protein binding;phosphatidylcholine transporter activity;phosphatidylinositol transporter activity;receptor tyrosine kinase binding;phosphatidylcholine binding;phosphatidylinositol binding;phosphatidic acid binding