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.

not_specified (44 variants)
not_provided (2 variants)

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. These statistics are base on transcript: NM_000006691.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			42 clinvar	4 clinvar		46
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	42	4	0

Loading clinvar variants...

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