LYPD3

LY6/PLAUR domain containing 3, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 19:43460787-43465608

Links

ENSG00000124466 ∙ NCBI:27076 ∙ OMIM:609484 ∙ HGNC:24880 ∙ Uniprot:O95274 ∙ 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 LYPD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYPD3 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					2	2
missense			22	1	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	3

Variants in LYPD3

This is a list of pathogenic ClinVar variants found in the LYPD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-43461375-G-A			Benign (Dec 28, 2017)
19-43461386-G-A		not specified	Uncertain significance (Dec 21, 2022)
19-43461394-A-G		not specified	Uncertain significance (Jun 24, 2022)
19-43461494-C-T		not specified	Uncertain significance (Nov 09, 2023)
19-43461518-C-T		not specified	Uncertain significance (Nov 18, 2023)
19-43461524-G-A		not specified	Uncertain significance (Jan 17, 2024)
19-43461577-A-G		not specified	Likely benign (Jun 03, 2022)
19-43461652-G-T			Benign (Jan 19, 2018)
19-43461724-G-C		not specified	Uncertain significance (Aug 08, 2022)
19-43461734-G-A		not specified	Uncertain significance (Jun 23, 2023)
19-43461763-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-43461778-G-C		not specified	Uncertain significance (Nov 08, 2024)
19-43461812-C-T		not specified	Uncertain significance (Feb 27, 2023)
19-43461826-G-A		not specified	Uncertain significance (Apr 19, 2023)
19-43463212-C-A		not specified	Uncertain significance (Feb 22, 2025)
19-43463646-C-A		not specified	Uncertain significance (May 08, 2024)
19-43463661-T-C		not specified	Uncertain significance (Aug 04, 2023)
19-43463694-A-C		not specified	Uncertain significance (Dec 28, 2024)
19-43463698-C-A		not specified	Uncertain significance (Dec 25, 2024)
19-43463751-A-T		not specified	Uncertain significance (Nov 21, 2024)
19-43463768-G-C		not specified	Uncertain significance (Aug 22, 2023)
19-43464334-C-T		not specified	Uncertain significance (Feb 20, 2025)
19-43464369-G-A		not specified	Uncertain significance (Aug 21, 2023)
19-43464382-C-T		not specified	Uncertain significance (Sep 06, 2022)
19-43464391-T-C		not specified	Uncertain significance (Jul 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYPD3	protein_coding	protein_coding	ENST00000244333	5	4874

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.83e-11	0.00898	125653	1	90	125744	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0820	206	209	0.984	0.0000117	2169
Missense in Polyphen		73	75.605	0.96554		826
Synonymous	0.527	86	92.4	0.930	0.00000512	764
Loss of Function	-1.25	14	9.78	1.43	4.20e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000646	0.000645
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000481	0.000457
Middle Eastern	0.000327	0.000326
South Asian	0.000398	0.000392
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Supports cell migration. May be involved in urothelial cell-matrix interactions. May be involved in tumor progression. {ECO:0000269|PubMed:11179665, ECO:0000269|PubMed:11245483, ECO:0000269|PubMed:12592373, ECO:0000269|PubMed:15012588}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.796
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.173
• hipred: N
• hipred_score: 0.146
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.450

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lypd3
• Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; hematopoietic system phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm

Gene ontology

• Biological process: cell-matrix adhesion
• Cellular component: extracellular region;extracellular space;plasma membrane;integral component of membrane;anchored component of plasma membrane
• Molecular function: laminin binding