LYPD6

LY6/PLAUR domain containing 6, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 2:149329985-149474138

Links

ENSG00000187123 ∙ NCBI:130574 ∙ OMIM:613359 ∙ HGNC:28751 ∙ Uniprot:Q86Y78 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LYPD6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYPD6 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					1	1
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	1

Variants in LYPD6

This is a list of pathogenic ClinVar variants found in the LYPD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-149437773-C-T		not specified	Uncertain significance (May 12, 2024)
2-149449066-G-A		not specified	Uncertain significance (Jul 11, 2023)
2-149468705-C-T		not specified	Uncertain significance (Dec 13, 2022)
2-149468745-C-T			Benign (Dec 18, 2018)
2-149468747-G-T		not specified	Uncertain significance (Feb 07, 2023)
2-149470731-C-G		not specified	Uncertain significance (Aug 29, 2022)
2-149470749-A-G		not specified	Uncertain significance (Jun 02, 2024)
2-149470759-C-T		not specified	Uncertain significance (Apr 28, 2022)
2-149470762-C-T		not specified	Uncertain significance (Jun 28, 2022)
2-149470776-C-G		not specified	Uncertain significance (Jun 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYPD6	protein_coding	protein_coding	ENST00000334166	4	144164

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000402	0.390	125636	0	94	125730	0.000374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.330	87	96.1	0.905	0.00000505	1090
Missense in Polyphen		30	31.56	0.95058		347
Synonymous	0.332	34	36.5	0.930	0.00000191	336
Loss of Function	0.438	9	10.5	0.854	7.63e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00206	0.00206
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000986	0.0000980
Other	0.000494	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a modulator of nicotinic acetylcholine receptors (nAChRs) function in the brain. Inhibits nicotine-induced Ca(2+) influx through nAChRs (PubMed:27344019). Acts as a positive regulator of Wnt/beta-catenin signaling (By similarity). {ECO:0000250|UniProtKB:Q66IA6, ECO:0000269|PubMed:27344019}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.369
• hipred: N
• hipred_score: 0.350
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lypd6
• Phenotype: 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); reproductive 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); endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: lypd6
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: regulation of neurotransmitter receptor activity;negative regulation of signaling receptor activity
• Cellular component: extracellular region;cytoplasm;plasma membrane;cell junction;anchored component of membrane;neuron projection;membrane raft;synapse
• Molecular function: protein binding;acetylcholine receptor inhibitor activity