PLBD1

phospholipase B domain containing 1

Basic information

Region (hg38): 12:14503661-14567883

Links

ENSG00000121316 ∙ NCBI:79887 ∙ OMIM:618486 ∙ HGNC:26215 ∙ Uniprot:Q6P4A8 ∙ 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 PLBD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLBD1 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			23	4		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	4	0

Variants in PLBD1

This is a list of pathogenic ClinVar variants found in the PLBD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-14503872-C-T		not specified	Likely benign (Aug 08, 2022)
12-14503873-G-A		not specified	Uncertain significance (Sep 29, 2023)
12-14503917-T-A		not specified	Uncertain significance (Sep 12, 2023)
12-14503944-A-G		not specified	Uncertain significance (Mar 18, 2024)
12-14506214-C-G		not specified	Uncertain significance (Mar 25, 2024)
12-14506941-C-T		not specified	Uncertain significance (Mar 22, 2022)
12-14506950-T-C		not specified	Uncertain significance (Feb 28, 2023)
12-14506986-T-C		not specified	Uncertain significance (Sep 01, 2021)
12-14506989-C-T		not specified	Uncertain significance (Jul 20, 2021)
12-14506992-C-T			Likely benign (Jan 01, 2023)
12-14507038-C-T		not specified	Uncertain significance (Jun 29, 2023)
12-14507100-T-C		not specified	Uncertain significance (Jul 13, 2021)
12-14511302-T-C		not specified	Uncertain significance (Mar 31, 2024)
12-14511335-T-C		not specified	Uncertain significance (Jun 02, 2023)
12-14511391-T-C		not specified	Uncertain significance (Sep 20, 2023)
12-14511576-C-T		not specified	Uncertain significance (Feb 27, 2024)
12-14511577-G-A		not specified	Uncertain significance (May 25, 2022)
12-14511699-G-C		not specified	Uncertain significance (Dec 08, 2023)
12-14535709-A-G		not specified	Uncertain significance (Nov 09, 2023)
12-14536571-T-C		not specified	Uncertain significance (Nov 10, 2022)
12-14536581-C-T		not specified	Uncertain significance (Feb 02, 2022)
12-14536608-T-C		not specified	Uncertain significance (Feb 15, 2023)
12-14536635-T-C		not specified	Uncertain significance (Jan 03, 2024)
12-14540826-T-C		not specified	Uncertain significance (Apr 14, 2023)
12-14542283-T-C		not specified	Uncertain significance (Sep 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLBD1	protein_coding	protein_coding	ENST00000240617	11	64689

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.18e-16	0.0203	125564	0	184	125748	0.000732

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.778	253	290	0.872	0.0000146	3616
Missense in Polyphen		112	143.67	0.77956		1734
Synonymous	-0.0913	106	105	1.01	0.00000512	1031
Loss of Function	0.440	26	28.5	0.911	0.00000149	336

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000929	0.000928
Ashkenazi Jewish	0.000595	0.000595
East Asian	0.00104	0.00103
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000708	0.000703
Middle Eastern	0.00104	0.00103
South Asian	0.00177	0.00177
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: In view of the small size of the putative binding pocket, it has been proposed that it may act as an amidase or a peptidase (By similarity). Exhibits a weak phospholipase activity, acting on various phospholipids, including phosphatidylcholine, phosphatidylinositol, phosphatidylethanolamine and lysophospholipids. {ECO:0000250, ECO:0000269|PubMed:19019078}.
• Pathway: Acyl chain remodelling of PI;Metabolism of lipids;Metabolism;Acyl chain remodelling of PC;Glycerophospholipid biosynthesis;Phospholipid metabolism;Hydrolysis of LPC;Acyl chain remodelling of PE (Consensus)

Intolerance Scores

• loftool: 0.909
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.88

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.125

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plbd1
• Phenotype: normal phenotype

Gene ontology

• Biological process: phospholipid metabolic process;lipid catabolic process;phosphatidylinositol acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling
• Cellular component: extracellular space;lysosome;cytosol
• Molecular function: lysophospholipase activity;phospholipase A2 activity