PI3

peptidase inhibitor 3, the group of WAP four-disulfide core domain containing

Basic information

Region (hg38): 20:45174901-45176544

Links

ENSG00000124102 ∙ NCBI:5266 ∙ OMIM:182257 ∙ HGNC:8947 ∙ Uniprot:P19957 ∙ 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 PI3 gene.

• Inborn genetic diseases (4 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PI3 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			2	2		4
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	2	0

Variants in PI3

This is a list of pathogenic ClinVar variants found in the PI3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45174923-A-G			Uncertain significance (Jul 10, 2017)
20-45175943-A-T		not specified	Uncertain significance (Feb 05, 2024)
20-45175954-A-C		not specified	Uncertain significance (Feb 05, 2024)
20-45175969-A-G		not specified	Likely benign (Nov 19, 2022)
20-45176005-C-T		not specified	Uncertain significance (Nov 17, 2022)
20-45176026-G-A		not specified	Likely benign (Apr 12, 2022)
20-45176031-G-A		not specified	Uncertain significance (Jul 27, 2021)
20-45176031-G-T		not specified	Uncertain significance (Jan 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PI3	protein_coding	protein_coding	ENST00000243924	2	1669

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.170	0.655	125726	0	8	125734	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0997	67	69.3	0.966	0.00000418	749
Missense in Polyphen		12	18.053	0.66471		211
Synonymous	-0.336	30	27.7	1.08	0.00000189	241
Loss of Function	0.816	1	2.35	0.426	1.01e-7	28

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Neutrophil and pancreatic elastase-specific inhibitor of skin. It may prevent elastase-mediated tissue proteolysis.
• Pathway: Keratinization;Developmental Biology;Antimicrobial peptides;Innate Immune System;Immune System;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.396

Intolerance Scores

• loftool: 0.524
• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.99

Haploinsufficiency Scores

• pHI: 0.351
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.764

Gene Damage Prediction

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

Gene ontology

• Biological process: copulation;negative regulation of endopeptidase activity;peptide cross-linking;antimicrobial humoral response;cornification
• Cellular component: cornified envelope;extracellular region;cytosol;extracellular matrix
• Molecular function: endopeptidase inhibitor activity;serine-type endopeptidase inhibitor activity;structural constituent of epidermis