PITPNM3

PITPNM family member 3, the group of Atypical chemokine receptors|Phosphatidylinositol transfer proteins

Basic information

Region (hg38): 17:6451263-6556555

Previous symbols: [ "CORD5" ]

Links

ENSG00000091622 ∙ NCBI:83394 ∙ OMIM:608921 ∙ HGNC:21043 ∙ Uniprot:Q9BZ71 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cone-rod dystrophy (Supportive), mode of inheritance: AD
• cone-rod dystrophy 5 (Strong), mode of inheritance: AD
• cone-rod dystrophy 5 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cone-rod dystrophy 5	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	8586428; 17377520; 18188949; 22405330

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PITPNM3 gene.

• Cone dystrophy (1 variants)
• Cerebral arteriovenous malformation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PITPNM3 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			10	184	12	206
missense			318	10	5	333
nonsense	2	1	2			5
start loss						0
frameshift			1			1
inframe indel			7			7
splice donor/acceptor (+/-2bp)			3			3
splice region			21	26	6	53
non coding			84	98	63	245
Total	2	1	425	292	80

Variants in PITPNM3

This is a list of pathogenic ClinVar variants found in the PITPNM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-6451291-G-A		Cone-rod dystrophy 5	Uncertain significance (Jan 12, 2018)
17-6451460-C-T		Cone-rod dystrophy 5	Benign (Jan 13, 2018)
17-6451576-G-A		Cone-rod dystrophy 5	Uncertain significance (Jan 13, 2018)
17-6451604-C-T		Cone-rod dystrophy 5	Benign (Jan 12, 2018)
17-6451615-C-T		Cone-rod dystrophy 5	Benign (Jan 13, 2018)
17-6451630-C-T		Cone-rod dystrophy 5	Benign (Jan 13, 2018)
17-6451631-C-T		Cone-rod dystrophy 5	Uncertain significance (Jan 12, 2018)
17-6451632-C-G		Cone-rod dystrophy 5	Uncertain significance (Jan 13, 2018)
17-6451645-T-C		Cone-rod dystrophy 5	Benign (Jan 12, 2018)
17-6451653-T-G		Cone-rod dystrophy 5	Benign (Jan 12, 2018)
17-6451777-C-T		Cone-rod dystrophy 5	Benign (Jan 12, 2018)
17-6451782-GT-G		Cone-Rod Dystrophy, Dominant	Benign (Jun 14, 2016)
17-6451797-G-A		Cone-rod dystrophy 5	Benign (Jan 13, 2018)
17-6451829-G-A		Cone-rod dystrophy 5	Benign (Jan 13, 2018)
17-6451873-AC-A		Cone-Rod Dystrophy, Dominant	Uncertain significance (Jun 14, 2016)
17-6451873-A-AC		Cone-Rod Dystrophy, Dominant	Uncertain significance (Jun 14, 2016)
17-6451874-C-CCG		Cone-Rod Dystrophy, Dominant	Uncertain significance (Jun 14, 2016)
17-6451876-C-G		Cone-rod dystrophy 5	Uncertain significance (Jan 13, 2018)
17-6451880-C-A		Cone-rod dystrophy 5	Uncertain significance (Jan 12, 2018)
17-6451881-C-CA		Cone-Rod Dystrophy, Dominant	Uncertain significance (Jun 14, 2016)
17-6451882-C-CA		Cone-Rod Dystrophy, Dominant	Uncertain significance (Jun 14, 2016)
17-6451884-C-G			Benign (Jul 01, 2022)
17-6451884-CCG-C		Cone-Rod Dystrophy, Dominant	Uncertain significance (Jun 14, 2016)
17-6451884-C-CG		Cone-Rod Dystrophy, Dominant	Uncertain significance (Jun 14, 2016)
17-6451884-C-CT		Cone-Rod Dystrophy, Dominant	Uncertain significance (Jun 14, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PITPNM3	protein_coding	protein_coding	ENST00000262483	20	105231

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000776	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.01	460	599	0.768	0.0000399	6334
Missense in Polyphen		84	151.07	0.55602		1616
Synonymous	-0.777	279	263	1.06	0.0000186	1975
Loss of Function	5.63	4	44.5	0.0899	0.00000239	482

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000122	0.000121
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000799	0.0000791
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 phosphatidylinositol and phosphatidylcholine between membranes (in vitro) (By similarity). Binds calcium ions. {ECO:0000250}.
• Pathway: Metabolism of lipids;Metabolism;Synthesis of PI;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.0640
• rvis_EVS: -1.39
• rvis_percentile_EVS: 4.31

Haploinsufficiency Scores

• pHI: 0.537
• hipred: Y
• hipred_score: 0.768
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.456

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pitpnm3

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;endoplasmic reticulum to Golgi vesicle-mediated transport;phospholipid transport
• Cellular component: cytosol;endomembrane system;membrane;COPII-coated ER to Golgi transport vesicle;cell projection;cell body
• Molecular function: phospholipase activity;calcium ion binding;protein binding;lipid binding;phosphatidylinositol transporter activity;receptor tyrosine kinase binding