PLCXD2

phosphatidylinositol specific phospholipase C X domain containing 2

Basic information

Region (hg38): 3:111674675-111846447

Links

ENSG00000240891 ∙ NCBI:257068 ∙ OMIM:617015 ∙ HGNC:26462 ∙ Uniprot:Q0VAA5 ∙ 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 PLCXD2 gene.

• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLCXD2 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	10	1	0

Variants in PLCXD2

This is a list of pathogenic ClinVar variants found in the PLCXD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-111675292-T-C		not specified	Uncertain significance (Nov 09, 2022)
3-111707945-C-G		not specified	Uncertain significance (Jan 17, 2024)
3-111707967-C-G		not specified	Uncertain significance (Sep 22, 2022)
3-111707992-C-T		not specified	Uncertain significance (Dec 13, 2023)
3-111708001-G-A		not specified	Uncertain significance (Jun 01, 2023)
3-111708094-G-A		not specified	Uncertain significance (May 17, 2023)
3-111708168-G-T		not specified	Uncertain significance (Jan 10, 2022)
3-111708204-T-A		not specified	Uncertain significance (Dec 01, 2022)
3-111708277-A-G		not specified	Uncertain significance (Jun 16, 2023)
3-111708279-C-T		not specified	Uncertain significance (Jun 28, 2022)
3-111708297-C-T		not specified	Uncertain significance (Nov 13, 2023)
3-111708298-G-A		not specified	Uncertain significance (Nov 04, 2022)
3-111708361-G-A		not specified	Likely benign (Dec 28, 2023)
3-111713911-T-A		not specified	Uncertain significance (Jan 17, 2024)
3-111713915-A-G		not specified	Uncertain significance (Dec 09, 2023)
3-111713949-G-T		not specified	Uncertain significance (Jan 03, 2024)
3-111732624-G-A		not specified	Likely benign (Mar 06, 2023)
3-111845896-G-A		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLCXD2	protein_coding	protein_coding	ENST00000477665	4	171772

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.66e-8	0.222	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.337	163	176	0.928	0.00000973	1997
Missense in Polyphen		66	76.204	0.86609		896
Synonymous	0.626	64	70.7	0.905	0.00000361	615
Loss of Function	0.341	12	13.3	0.899	7.19e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00104	0.00104
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000272	0.000272
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000272	0.000272
South Asian	0.000294	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.341
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.251
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plcxd2

Zebrafish Information Network

• Gene name: plcxd2
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

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