PLB1

phospholipase B1, the group of Phospholipases

Basic information

Region (hg38): 2:28457144-28644142

Links

ENSG00000163803 ∙ NCBI:151056 ∙ OMIM:610179 ∙ HGNC:30041 ∙ Uniprot:Q6P1J6 ∙ 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 PLB1 gene.

• Inborn genetic diseases (72 variants)
• not provided (41 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLB1 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				6	4	10
missense			71	7	14	92
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				2		2
splice region				5		5
non coding				1	3	4
Total	0	0	71	16	21

Variants in PLB1

This is a list of pathogenic ClinVar variants found in the PLB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-28496125-G-A		not specified	Likely benign (Oct 17, 2023)
2-28518490-T-C		not specified	Uncertain significance (Jan 24, 2024)
2-28518509-G-C		not specified	Uncertain significance (Apr 14, 2022)
2-28525298-A-G			Benign (Apr 24, 2018)
2-28525924-G-A		not specified	Uncertain significance (Apr 26, 2023)
2-28529326-A-T		not specified	Uncertain significance (Jan 05, 2022)
2-28529381-G-A			Likely benign (May 08, 2018)
2-28529405-T-C			Benign/Likely benign (Dec 01, 2022)
2-28529744-G-T		not specified	Uncertain significance (Jun 11, 2021)
2-28529756-G-T			Benign (Dec 31, 2019)
2-28529787-T-G			Likely benign (May 23, 2018)
2-28532127-A-T		not specified	Uncertain significance (Sep 22, 2023)
2-28532154-G-A		not specified	Uncertain significance (Dec 27, 2023)
2-28532176-G-A			Likely benign (Nov 14, 2018)
2-28538331-G-T		not specified	Uncertain significance (Sep 06, 2022)
2-28538332-C-T		not specified	Uncertain significance (Jun 23, 2023)
2-28538337-G-A		not specified	Likely benign (Mar 17, 2023)
2-28538343-G-A		not specified	Uncertain significance (Dec 22, 2023)
2-28538371-T-C		not specified	Uncertain significance (Feb 12, 2024)
2-28539165-G-A		not specified	Uncertain significance (Jan 31, 2023)
2-28540373-C-A		not specified	Uncertain significance (Nov 18, 2022)
2-28540407-G-A		not specified	Uncertain significance (Aug 02, 2021)
2-28541705-A-C			Likely benign (Dec 31, 2019)
2-28541711-C-T		not specified	Uncertain significance (Sep 09, 2021)
2-28541736-C-A		not specified	Uncertain significance (Jun 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLB1	protein_coding	protein_coding	ENST00000327757	58	186643

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.73e-72	2.99e-12	124972	0	776	125748	0.00309

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.588	866	819	1.06	0.0000450	9542
Missense in Polyphen		260	251.98	1.0318		3037
Synonymous	-1.84	367	325	1.13	0.0000192	2778
Loss of Function	-0.413	107	102	1.04	0.00000532	1103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00495	0.00495
Ashkenazi Jewish	0.00688	0.00687
East Asian	0.00518	0.00518
Finnish	0.00254	0.00254
European (Non-Finnish)	0.00325	0.00324
Middle Eastern	0.00518	0.00518
South Asian	0.00184	0.00183
Other	0.00212	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Membrane-associated phospholipase. Exhibits a calcium- independent broad substrate specificity including phospholipase A2/lysophospholipase activity. Preferential hydrolysis at the sn-2 position of diacylphospholipids and diacyglycerol, whereas it shows no positional specificity toward triacylglycerol. Exhibits also esterase activity toward p-nitrophenyl. May act on the brush border membrane to facilitate the absorption of digested lipids (By similarity). {ECO:0000250}.
• Pathway: Ether lipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Vitamin digestion and absorption - Homo sapiens (human);alpha-Linolenic acid metabolism - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Linoleic acid metabolism - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;Metabolism of lipids;Metabolism;phospholipases;Acyl chain remodelling of PC;Metabolism of vitamins and cofactors;Retinoid metabolism and transport;Glycerophospholipid biosynthesis;Phospholipid metabolism;G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 1.00
• rvis_EVS: 1.21
• rvis_percentile_EVS: 93.06

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.123
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.728

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plb1

Gene ontology

• Biological process: retinoid metabolic process;phospholipid metabolic process;lipid catabolic process;phosphatidylcholine acyl-chain remodeling;retinol metabolic process;positive regulation of acrosome reaction
• Cellular component: plasma membrane;integral component of membrane;apical plasma membrane;brush border membrane
• Molecular function: lysophospholipase activity;phospholipase A2 activity;retinyl-palmitate esterase activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)