LYPD4

LY6/PLAUR domain containing 4, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 19:41837074-41844697

Links

ENSG00000273111 ∙ NCBI:147719 ∙ ∙ HGNC:28659 ∙ Uniprot:Q6UWN0 ∙ 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 LYPD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYPD4 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in LYPD4

This is a list of pathogenic ClinVar variants found in the LYPD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-41837232-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-41837256-C-G		not specified	Uncertain significance (Mar 18, 2024)
19-41837262-T-C		not specified	Uncertain significance (Oct 12, 2022)
19-41837306-C-T		not specified	Uncertain significance (Dec 21, 2022)
19-41838045-G-A		not specified	Uncertain significance (Sep 30, 2021)
19-41838054-C-A		not specified	Uncertain significance (Jun 11, 2024)
19-41838130-A-T		not specified	Uncertain significance (Dec 21, 2022)
19-41838144-C-T		not specified	Uncertain significance (Apr 29, 2024)
19-41838148-C-G		not specified	Uncertain significance (Nov 16, 2022)
19-41838153-C-A		not specified	Uncertain significance (May 30, 2024)
19-41838192-T-C		not specified	Uncertain significance (May 25, 2022)
19-41838913-C-T		not specified	Uncertain significance (May 15, 2024)
19-41838992-C-T		not specified	Uncertain significance (Sep 22, 2023)
19-41839003-T-C		not specified	Uncertain significance (Oct 03, 2022)
19-41839257-T-C		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.0974

Intolerance Scores

• loftool: 0.848
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.49

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.165

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lypd4

Gene ontology

• Cellular component: extracellular region;plasma membrane;anchored component of membrane