PLBD2

phospholipase B domain containing 2

Basic information

Region (hg38): 12:113358566-113391629

Links

ENSG00000151176 ∙ NCBI:196463 ∙ OMIM:620097 ∙ HGNC:27283 ∙ Uniprot:Q8NHP8 ∙ 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 PLBD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLBD2 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			48	1		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	48	1	0

Variants in PLBD2

This is a list of pathogenic ClinVar variants found in the PLBD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-113358614-T-G		not specified	Uncertain significance (Sep 27, 2022)
12-113358619-T-A		not specified	Uncertain significance (Dec 05, 2024)
12-113358625-C-A		not specified	Uncertain significance (Oct 06, 2021)
12-113358646-G-C		not specified	Uncertain significance (Oct 05, 2023)
12-113358658-G-A		not specified	Uncertain significance (Mar 29, 2024)
12-113358709-G-T		not specified	Uncertain significance (Sep 16, 2021)
12-113358730-G-T		not specified	Uncertain significance (May 29, 2024)
12-113358734-C-T		not specified	Uncertain significance (Dec 21, 2022)
12-113358763-G-A		not specified	Uncertain significance (Oct 04, 2024)
12-113358778-C-T		not specified	Uncertain significance (Nov 28, 2024)
12-113358785-G-T		not specified	Uncertain significance (May 23, 2023)
12-113358787-T-G		not specified	Uncertain significance (Nov 02, 2023)
12-113358812-G-A		not specified	Uncertain significance (Oct 05, 2023)
12-113358880-C-A		not specified	Uncertain significance (Apr 09, 2024)
12-113369144-G-A		not specified	Uncertain significance (Oct 26, 2022)
12-113369183-G-A		not specified	Uncertain significance (Jun 28, 2024)
12-113372700-G-A		not specified	Uncertain significance (Dec 30, 2023)
12-113372721-G-A		not specified	Uncertain significance (Dec 17, 2021)
12-113372736-T-G		not specified	Uncertain significance (Mar 20, 2024)
12-113374543-G-A		not specified	Uncertain significance (Oct 29, 2024)
12-113374795-T-C		not specified	Uncertain significance (Nov 09, 2023)
12-113374900-T-C		not specified	Uncertain significance (Jan 25, 2023)
12-113374948-A-G		not specified	Uncertain significance (Apr 24, 2024)
12-113374962-C-T		not specified	Uncertain significance (Sep 20, 2023)
12-113374963-G-A		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLBD2	protein_coding	protein_coding	ENST00000280800	12	30833

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.72e-11	0.593	125575	0	173	125748	0.000688

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	266	327	0.813	0.0000193	3761
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000371	0.000366
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00418	0.00417
European (Non-Finnish)	0.000529	0.000501
Middle Eastern	0.000109	0.000109
South Asian	0.000335	0.000327
Other	0.000993	0.000978

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.907
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.71

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.301
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.359

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plbd2

Gene ontology

• Biological process: lipid catabolic process
• Cellular component: lysosomal lumen;extracellular exosome
• Molecular function: hydrolase activity