PNLIPRP3

pancreatic lipase related protein 3, the group of Lipases

Basic information

Region (hg38): 10:116427846-116477957

Links

ENSG00000203837 ∙ NCBI:119548 ∙ ∙ HGNC:23492 ∙ Uniprot:Q17RR3 ∙ 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 PNLIPRP3 gene.

• Inborn genetic diseases (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNLIPRP3 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	1		12
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	1	0

Variants in PNLIPRP3

This is a list of pathogenic ClinVar variants found in the PNLIPRP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-116428026-G-C		not specified	Uncertain significance (Jan 16, 2024)
10-116436737-G-A		not specified	Uncertain significance (Jan 11, 2023)
10-116436822-C-T		not specified	Uncertain significance (Nov 04, 2022)
10-116436825-G-A		Inborn genetic diseases	Uncertain significance (Nov 12, 2021)
10-116436843-T-C		not specified	Uncertain significance (Jan 08, 2024)
10-116443065-C-T		not specified	Uncertain significance (Oct 20, 2023)
10-116443095-A-G			Uncertain significance (Feb 08, 2023)
10-116443118-C-T		not specified	Uncertain significance (Dec 20, 2023)
10-116443119-G-A		not specified	Uncertain significance (Apr 07, 2023)
10-116444412-A-T		not specified	Uncertain significance (Dec 15, 2023)
10-116444422-A-G		not specified	Uncertain significance (Mar 07, 2023)
10-116444457-G-C		not specified	Uncertain significance (Apr 25, 2022)
10-116455782-C-A		not specified	Uncertain significance (Dec 17, 2023)
10-116455807-T-C		not specified	Likely benign (Feb 12, 2024)
10-116460983-C-A		not specified	Uncertain significance (Jan 26, 2022)
10-116461177-C-T		not specified	Uncertain significance (Feb 01, 2023)
10-116461214-T-A		not specified	Uncertain significance (Dec 01, 2023)
10-116461226-C-A		not specified	Uncertain significance (Dec 27, 2023)
10-116466140-C-T		not specified	Uncertain significance (Dec 18, 2023)
10-116469206-A-G		not specified	Uncertain significance (Dec 08, 2023)
10-116469291-A-G		not specified	Uncertain significance (Jun 07, 2023)
10-116471806-G-A		not specified	Likely benign (May 23, 2023)
10-116476659-C-T		not specified	Uncertain significance (Dec 12, 2023)
10-116476692-G-A		not specified	Uncertain significance (Oct 20, 2023)
10-116476714-A-G		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PNLIPRP3	protein_coding	protein_coding	ENST00000369230	12	50091

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.17e-11	0.237	114132	382	11232	125746	0.0473

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0586	251	248	1.01	0.0000123	3072
Missense in Polyphen		78	78.502	0.9936		922
Synonymous	0.177	82	84.1	0.975	0.00000420	847
Loss of Function	0.865	19	23.5	0.807	0.00000117	300

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.164	0.101
Ashkenazi Jewish	0.0765	0.0759
East Asian	0.00113	0.00109
Finnish	0.0884	0.0879
European (Non-Finnish)	0.0568	0.0566
Middle Eastern	0.00113	0.00109
South Asian	0.0158	0.0155
Other	0.0537	0.0515

dbNSFP

Source: dbNSFP

• Pathway: Glycerolipid metabolism - Homo sapiens (human);triacylglycerol degradation;Digestion of dietary lipid;Digestion;Digestion and absorption (Consensus)

Recessive Scores

• pRec: 0.0654

Intolerance Scores

• loftool: 0.370
• rvis_EVS: 1.31
• rvis_percentile_EVS: 94.01

Haploinsufficiency Scores

• pHI: 0.0485
• hipred: N
• hipred_score: 0.112
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.122

Gene Damage Prediction

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

Gene ontology

• Biological process: lipid catabolic process
• Cellular component: extracellular region
• Molecular function: triglyceride lipase activity