PLBD2

protein-coding

phospholipase B domain containing 2

Gene summary

Predicted to enable glycerophospholipase activity. Predicted to be involved in lipid catabolic process. Located in extracellular exosome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_173542.4

Inheritance

—

ClinVar variants

U:101B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr12:113,358,566-113,391,629

External References & Databases

Ensembl (ENSG00000151176)

Transcript & Mutation Effects

hg38 • Region Span ~33.1 kb

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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 PLBD2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 94

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173542.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			90 clinvar	4 clinvar		94
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	101	6	0	107

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173542.4	RefSeq	NP_775813.2	12	MANE Select
ENST00000280800.5	Ensembl	ENSP00000280800.3	12	MANE Select
NM_001159727.2	RefSeq	NP_001153199.1	11	Standard
ENST00000545182.6	Ensembl	ENSP00000443463.2	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

lipid catabolic process

Molecular Function

hydrolase activity

Cellular Component

lysosomal lumen
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000280800
Coding exons: 12
Length: 30833
Individuals with no LoFs: 125575
Homozygous LoFs: 0
Heterozygous LoFs: 173
Defined: 125748
p: 0.000688

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.20	266	327	0.813	0.0000193	3761
Missense (PolyPhen)		108	139.06	0.77664		1531
Synonymous	1.50	119	142	0.839	0.00000889	1189
Loss of Function	1.42	21	29.3	0.717	0.00000155	301

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.0042	0.0042	notable
European (Non-Finnish)	0.00053	0.00050	rare
South Asian	0.00033	0.00033	rare
Other	0.00099	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative phospholipase. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.907
RVIS EVS: -0.27
RVIS percentile EVS: 34.71

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.359

Gene Damage Prediction

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