PLCXD3

phosphatidylinositol specific phospholipase C X domain containing 3

Basic information

Region (hg38): 5:41306952-41510601

Links

ENSG00000182836 ∙ NCBI:345557 ∙ OMIM:617016 ∙ HGNC:31822 ∙ Uniprot:Q63HM9 ∙ 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 PLCXD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLCXD3 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in PLCXD3

This is a list of pathogenic ClinVar variants found in the PLCXD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-41313666-G-A		not specified	Uncertain significance (Oct 29, 2021)
5-41381853-C-T		not specified	Uncertain significance (Jan 26, 2022)
5-41381880-G-C		not specified	Uncertain significance (Jun 12, 2023)
5-41381904-G-C		not specified	Uncertain significance (Mar 07, 2024)
5-41381971-C-T		not specified	Uncertain significance (Dec 30, 2023)
5-41381975-G-C		not specified	Uncertain significance (Apr 05, 2023)
5-41382013-C-T		not specified	Uncertain significance (Jul 12, 2023)
5-41382074-G-C		not specified	Uncertain significance (Apr 12, 2022)
5-41382145-T-C		not specified	Uncertain significance (Mar 21, 2024)
5-41382180-T-C		not specified	Uncertain significance (Dec 27, 2023)
5-41382231-T-C		not specified	Uncertain significance (Oct 12, 2022)
5-41382252-T-C		not specified	Uncertain significance (Dec 19, 2023)
5-41382321-G-T		not specified	Uncertain significance (Mar 07, 2024)
5-41382385-T-C		not specified	Uncertain significance (Jun 22, 2023)
5-41382454-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLCXD3	protein_coding	protein_coding	ENST00000377801	3	203675

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00891	0.942	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.135	166	171	0.971	0.00000823	2135
Missense in Polyphen		50	54.51	0.91726		731
Synonymous	-1.69	81	63.8	1.27	0.00000329	609
Loss of Function	1.70	5	11.1	0.449	5.40e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000276	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000628	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Ectoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.276
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.344
• hipred: N
• hipred_score: 0.447
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.321

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plcxd3

Gene ontology

• Biological process: signal transduction;lipid catabolic process
• Cellular component: cytoplasm
• Molecular function: phosphoric diester hydrolase activity