PITPNM1

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

Basic information

Region (hg38): 11:67491760-67506263

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.

not_specified (155 variants)
not_provided (9 variants)

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. These statistics are base on transcript: NM_000004910.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar	1 clinvar	6
missense			152 clinvar	3 clinvar	2 clinvar	157
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	152	8	3

Loading clinvar variants...

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