LYVE1

lymphatic vessel endothelial hyaluronan receptor 1

Basic information

Region (hg38): 11:10556966-10611689

Previous symbols: [ "XLKD1" ]

Links

ENSG00000133800 ∙ NCBI:10894 ∙ OMIM:605702 ∙ HGNC:14687 ∙ Uniprot:Q9Y5Y7 ∙ 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 LYVE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYVE1 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			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	0

Variants in LYVE1

This is a list of pathogenic ClinVar variants found in the LYVE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-10559149-T-C		not specified	Uncertain significance (May 31, 2023)
11-10559157-T-A			Uncertain significance (Feb 01, 2024)
11-10559169-G-C		not specified	Uncertain significance (Jan 18, 2022)
11-10559214-T-C		not specified	Uncertain significance (Nov 10, 2022)
11-10559852-C-T		not specified	Uncertain significance (Jul 25, 2023)
11-10559885-G-A		not specified	Uncertain significance (Apr 06, 2022)
11-10560507-C-A		not specified	Uncertain significance (Mar 07, 2024)
11-10560546-G-C		not specified	Uncertain significance (Nov 17, 2023)
11-10560566-G-T		not specified	Uncertain significance (Nov 17, 2023)
11-10560569-C-A		not specified	Uncertain significance (Feb 28, 2023)
11-10560578-A-G		not specified	Likely benign (Jun 29, 2023)
11-10560600-T-C		not specified	Uncertain significance (Oct 27, 2022)
11-10560647-G-A		not specified	Uncertain significance (Nov 17, 2022)
11-10563963-G-T		not specified	Uncertain significance (May 27, 2022)
11-10563981-G-C		not specified	Uncertain significance (Sep 30, 2021)
11-10564005-A-G		not specified	Uncertain significance (Nov 09, 2021)
11-10564026-G-A			Likely benign (Mar 01, 2023)
11-10564054-C-T		not specified	Uncertain significance (Jun 06, 2023)
11-10564062-T-C		not specified	Uncertain significance (Mar 28, 2024)
11-10564233-G-A		not specified	Uncertain significance (Mar 01, 2023)
11-10564281-G-T		not specified	Uncertain significance (Sep 30, 2021)
11-10564296-G-C		not specified	Uncertain significance (Nov 18, 2022)
11-10564335-G-T		not specified	Uncertain significance (Mar 31, 2024)
11-10564344-A-G		not specified	Uncertain significance (Jun 21, 2022)
11-10568451-C-T		not specified	Uncertain significance (Nov 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYVE1	protein_coding	protein_coding	ENST00000256178	6	54724

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.72e-7	0.405	125699	0	48	125747	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.186	162	169	0.960	0.00000814	2097
Missense in Polyphen		37	39.299	0.9415		523
Synonymous	-0.173	68	66.2	1.03	0.00000355	650
Loss of Function	0.636	11	13.5	0.813	6.56e-7	167

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000517	0.000517
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000265	0.000264
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ligand-specific transporter trafficking between intracellular organelles (TGN) and the plasma membrane. Plays a role in autocrine regulation of cell growth mediated by growth regulators containing cell surface retention sequence binding (CRS). May act as a hyaluronan (HA) transporter, either mediating its uptake for catabolism within lymphatic endothelial cells themselves, or its transport into the lumen of afferent lymphatic vessels for subsequent re-uptake and degradation in lymph nodes. {ECO:0000269|PubMed:10037799}.
• Pathway: Hyaluronan uptake and degradation;Hyaluronan metabolism;Metabolism of carbohydrates;Glycosaminoglycan metabolism;Metabolism (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• loftool: 0.830
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.450
• hipred: N
• hipred_score: 0.123
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.212

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lyve1
• Phenotype: immune system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: lyve1a
• Affected structure: thoracic duct
• Phenotype tag: abnormal
• Phenotype quality: agenesis

Gene ontology

• Biological process: cell-matrix adhesion;response to wounding;anatomical structure morphogenesis;hyaluronan catabolic process
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;extracellular exosome
• Molecular function: transmembrane signaling receptor activity;protein binding;hyaluronic acid binding;signaling receptor activity