PLCXD1

phosphatidylinositol specific phospholipase C X domain containing 1, the group of Pseudoautosomal region 1

Basic information

Region (hg38): Y:276322-303356

Links

ENSG00000292344 ∙ NCBI:55344 ∙ OMIM:300974 ∙ HGNC:23148 ∙ Uniprot:Q9NUJ7 ∙ 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 PLCXD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLCXD1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLCXD1	protein_coding	protein_coding	ENST00000381657	6	27035

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.31e-10	0.0566	125334	4	253	125591	0.00102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.53	292	227	1.28	0.0000172	2073
Missense in Polyphen		89	66.291	1.3426		709
Synonymous	-2.39	143	111	1.29	0.00000943	673
Loss of Function	-0.178	14	13.3	1.05	5.73e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00381	0.00381
Ashkenazi Jewish	0.00	0.00
East Asian	0.00827	0.00819
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000150
Middle Eastern	0.00827	0.00819
South Asian	0.000491	0.000425
Other	0.000653	0.000653

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.537
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.32

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.170
• ghis: 0.549

Essentials

• essential_gene_CRISPR: 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: Plcxd1

Gene ontology

• Biological process: lipid metabolic process
• Cellular component: cytoplasm
• Molecular function: phosphoric diester hydrolase activity