PIRT

phosphoinositide interacting regulator of transient receptor potential channels

Basic information

Region (hg38): 17:10822469-10838087

Links

ENSG00000233670 ∙ NCBI:644139 ∙ OMIM:612068 ∙ HGNC:37239 ∙ Uniprot:P0C851 ∙ 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 PIRT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIRT 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in PIRT

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

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

Position	Type	Phenotype	Significance	ClinVar
17-10825240-T-C		not specified	Uncertain significance (Feb 14, 2023)
17-10825275-G-A		not specified	Uncertain significance (Feb 23, 2023)
17-10825303-T-C		not specified	Uncertain significance (May 25, 2022)
17-10825337-C-G		not specified	Uncertain significance (Jan 16, 2024)
17-10825432-T-C		not specified	Uncertain significance (May 18, 2022)
17-10825441-C-T		not specified	Uncertain significance (Oct 17, 2023)
17-10825486-T-C		not specified	Uncertain significance (May 14, 2024)
17-10825518-G-A		not specified	Uncertain significance (Oct 10, 2023)
17-10825534-C-T		not specified	Uncertain significance (May 14, 2024)
17-10825583-G-T		not specified	Uncertain significance (Dec 28, 2022)
17-10825615-C-T		not specified	Uncertain significance (Sep 20, 2023)
17-10825623-T-C		not specified	Uncertain significance (Apr 25, 2022)
17-10825638-A-C		not specified	Uncertain significance (Oct 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIRT	protein_coding	protein_coding	ENST00000580256	1	15971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.580	0.380	124575	0	1	124576	0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0465	78	76.9	1.01	0.00000442	880
Missense in Polyphen		35	33.091	1.0577		396
Synonymous	-0.262	35	33.1	1.06	0.00000201	281
Loss of Function	1.52	0	2.68	0.00	1.13e-7	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit of TRPV1, a molecular sensor of noxious heat and capsaicin. Positively regulates TRPV1 channel activity via phosphatidylinositol 4,5-bisphosphate (PIP2). Binds various phosphoinositide, including phosphatidylinositol 4,5- bisphosphate (PIP2), but not phosphatidylinositol (PI) (By similarity). {ECO:0000250}.

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.219
• ghis: 0.452

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pirt
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: response to heat;phosphatidylinositol-mediated signaling;behavioral response to pain;positive regulation of cation channel activity
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: phosphatidylinositol-3,4,5-trisphosphate binding;ion channel binding;phosphatidylinositol bisphosphate binding