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.

not_specified (16 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_000194317.5. 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					1 clinvar	1
missense			16 clinvar			16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	16	0	1

Loading clinvar variants...

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

loftool
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