GeneBe

PLB1

protein-coding

phospholipase B1, the group of Phospholipases

Gene summary

This gene encodes a membrane-associated phospholipase that displays lysophospholipase and phospholipase A2 activities through removal of sn-1 and sn-2 fatty acids of glycerophospholipids. In addition, it displays lipase and retinyl ester hydrolase activities. The encoded protein is highly conserved and is composed of a large, glycosylated extracellular domain composed of four tandem homologous domains, followed by a hydrophobic segment that anchors the enzyme to the membrane and a short C-terminal cytoplasmic tail. This gene has been identified as a candidate rheumatoid arthritis risk gene. [provided by RefSeq, Jul 2016]

MANE transcript

NM_153021.5

Inheritance

—

ClinVar variants

U:244B:48

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 1.04

Max pathogenic AF

—

Genomic locus

chr2:28,457,145-28,644,142

External References & Databases

Ensembl (ENSG00000163803)NCBI Gene (151056)OMIM (610179)HGNC:30041GenCCUniProt (Q6P1J6)AlphaFoldClinVar (PLB1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~187.0 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PLB1 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 243
not providedTotal: 46
Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153021.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
10
clinvar
4
clinvar
 16
missense
233
clinvar
18
clinvar
14
clinvar
 265
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
9
clinvar
2
clinvar
 11
Total002443018292
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_153021.5RefSeqNP_694566.458MANE Select
ENST00000327757.10EnsemblENSP00000330442.558MANE Select
NM_001170585.2RefSeqNP_001164056.157Standard
ENST00000404858.5EnsemblENSP00000384187.157Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • 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)

Biological Process

  • retinoid metabolic process
  • phospholipid metabolic process
  • lipid catabolic process
  • phosphatidylcholine acyl-chain remodeling
  • retinol metabolic process

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)

Cellular Component

  • plasma membrane
  • integral component of membrane
  • apical plasma membrane
  • brush border membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000327757
Coding exons
58
Length
186643
Individuals with no LoFs
124972
Homozygous LoFs
0
Heterozygous LoFs
776
Defined
125748
p
0.00309
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.5888668191.060.00004509542
Missense (PolyPhen)260251.981.03183037
Synonymous-1.843673251.130.00001922778
Loss of Function-0.4131071021.040.000005321103

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00280.0028notable
Latino/Admixed American0.00220.0022notable
Ashkenazi Jewish0.00690.0069notable
East Asian0.00520.0052notable
Finnish0.00250.0025notable
European (Non-Finnish)0.00330.0032notable
South Asian0.00180.0018notable
Other0.00210.0021notable

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec
0.115

Intolerance Scores

LoFtool
1.00
RVIS EVS
1.21
RVIS percentile EVS
93.06

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.728

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium
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