PNLIPRP1

pancreatic lipase related protein 1

Basic information

Region (hg38): 10:116590385-116609175

Links

ENSG00000187021 ∙ NCBI:5407 ∙ OMIM:604422 ∙ HGNC:9156 ∙ Uniprot:P54315 ∙ 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 PNLIPRP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNLIPRP1 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			31	2		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	2	0

Variants in PNLIPRP1

This is a list of pathogenic ClinVar variants found in the PNLIPRP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-116591788-G-A		not specified	Uncertain significance (Apr 01, 2024)
10-116591792-A-G		not specified	Uncertain significance (Feb 10, 2022)
10-116591792-A-T		not specified	Uncertain significance (Jan 06, 2023)
10-116591797-G-C		not specified	Uncertain significance (Nov 18, 2023)
10-116591825-G-A		not specified	Uncertain significance (Apr 05, 2023)
10-116591878-G-A		not specified	Uncertain significance (Jan 31, 2024)
10-116591885-G-A		not specified	Uncertain significance (Dec 27, 2023)
10-116592465-T-C		not specified	Likely benign (Mar 15, 2024)
10-116592480-G-A		not specified	Uncertain significance (Jan 30, 2024)
10-116592517-G-C		not specified	Uncertain significance (Jan 24, 2024)
10-116592531-A-G		not specified	Uncertain significance (Jan 30, 2024)
10-116592536-T-C		not specified	Uncertain significance (Jan 10, 2023)
10-116594739-G-A		not specified	Likely benign (Apr 03, 2023)
10-116594830-G-T		not specified	Uncertain significance (Jul 27, 2022)
10-116596218-A-G		not specified	Uncertain significance (Aug 22, 2023)
10-116596232-C-T		not specified	Uncertain significance (Dec 21, 2023)
10-116596233-C-G		not specified	Uncertain significance (Feb 27, 2023)
10-116596233-C-T		not specified	Uncertain significance (Sep 13, 2023)
10-116596235-T-G		not specified	Uncertain significance (Jul 05, 2023)
10-116596268-G-C		not specified	Uncertain significance (May 06, 2022)
10-116596274-G-A		not specified	Uncertain significance (Sep 27, 2021)
10-116596294-C-G		not specified	Uncertain significance (Jan 07, 2022)
10-116597866-G-A		not specified	Uncertain significance (Jul 05, 2023)
10-116597876-G-A		not specified	Uncertain significance (May 27, 2022)
10-116597918-C-T		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PNLIPRP1	protein_coding	protein_coding	ENST00000528052	12	18791

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.09e-13	0.0808	125498	1	249	125748	0.000995

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0831	264	260	1.01	0.0000135	3082
Missense in Polyphen		88	85.304	1.0316		1021
Synonymous	-0.776	112	102	1.10	0.00000588	875
Loss of Function	0.640	22	25.5	0.863	0.00000135	288

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00401	0.00401
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.000435	0.000435
Finnish	0.000463	0.000462
European (Non-Finnish)	0.00109	0.00109
Middle Eastern	0.000435	0.000435
South Asian	0.000329	0.000327
Other	0.00180	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as inhibitor of dietary triglyceride digestion. Lacks detectable lipase activity towards triglycerides, diglycerides, phosphatidylcholine, galactolipids or cholesterol esters (in vitro) (By similarity). {ECO:0000250, ECO:0000269|PubMed:19824014}.
• Pathway: Glycerolipid metabolism - Homo sapiens (human);Fat digestion and absorption - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Glycerophospholipid metabolism;Digestion of dietary lipid;Digestion;Digestion and absorption (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.74

Haploinsufficiency Scores

• pHI: 0.355
• hipred: N
• hipred_score: 0.131

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0766

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pnliprp1

Gene ontology

• Biological process: lipid metabolic process
• Cellular component: extracellular region;extracellular space
• Molecular function: triglyceride lipase activity;calcium ion binding;lipase activity