LYPD1

LY6/PLAUR domain containing 1, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 2:132643285-132671579

Previous symbols: [ "LYPDC1" ]

Links

ENSG00000150551 ∙ NCBI:116372 ∙ OMIM:610450 ∙ HGNC:28431 ∙ Uniprot:Q8N2G4 ∙ 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 LYPD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYPD1 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			18	2	2	22
Total	0	0	20	2	2

Variants in LYPD1

This is a list of pathogenic ClinVar variants found in the LYPD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-132645123-C-A			Benign (Jul 10, 2017)
2-132645124-G-T		not specified	Uncertain significance (Dec 21, 2023)
2-132645145-A-C		not specified	Uncertain significance (Jun 07, 2024)
2-132645199-T-C		not specified	Uncertain significance (Mar 02, 2023)
2-132645284-C-T		not specified	Uncertain significance (Aug 22, 2023)
2-132645310-G-C		not specified	Uncertain significance (Apr 19, 2024)
2-132645337-C-A		not specified	Uncertain significance (Dec 02, 2022)
2-132645338-T-G		not specified	Uncertain significance (Dec 02, 2022)
2-132645341-A-C		not specified	Likely benign (Aug 21, 2023)
2-132645341-A-G		not specified	Uncertain significance (Nov 14, 2023)
2-132645376-G-A		not specified	Conflicting classifications of pathogenicity (Jul 26, 2018)
2-132645379-C-T		not specified	Uncertain significance (Dec 06, 2022)
2-132645393-C-A		not specified	Uncertain significance (Mar 01, 2024)
2-132645404-T-G		not specified	Uncertain significance (Nov 30, 2021)
2-132645416-C-G		not specified	Uncertain significance (Sep 17, 2021)
2-132645420-G-T		not specified	Uncertain significance (Dec 28, 2022)
2-132645421-C-T		not specified	Uncertain significance (Dec 28, 2022)
2-132645433-C-T		not specified	Likely benign (May 30, 2023)
2-132645474-A-T		not specified	Uncertain significance (Dec 03, 2021)
2-132645507-T-TAAG			Benign (Aug 20, 2018)
2-132645512-C-G		not specified	Uncertain significance (Aug 22, 2023)
2-132645545-A-G		not specified	Uncertain significance (Nov 06, 2023)
2-132645553-G-T		not specified	Uncertain significance (Feb 06, 2024)
2-132645560-C-T		not specified	Uncertain significance (Mar 11, 2024)
2-132646050-A-C		not specified	Uncertain significance (Nov 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYPD1	protein_coding	protein_coding	ENST00000397463	3	26727

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000554	0.481	124736	0	19	124755	0.0000762

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.498	63	75.1	0.838	0.00000390	912
Missense in Polyphen		37	47.373	0.78103		570
Synonymous	-1.51	44	33.0	1.34	0.00000201	270
Loss of Function	0.198	5	5.50	0.909	2.33e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000186	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000615	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000626	0.0000618
Middle Eastern	0.0000615	0.0000556
South Asian	0.000248	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Believed to act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro increases receptor desensitization and decreases affinity for ACh of alpha- 4:beta-2-containing nAChRs. May play a role in the intracellular trafficking of alpha-4:beta-2 and alpha-7-containing nAChRs and may inhibit their expression at the cell surface. May be involved in the control of anxiety. {ECO:0000250|UniProtKB:Q8BLC3}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Intolerance Scores

• loftool: 0.507
• rvis_EVS: 0.3
• rvis_percentile_EVS: 72.01

Haploinsufficiency Scores

• pHI: 0.217
• hipred: N
• hipred_score: 0.342
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lypd1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: behavioral fear response;synaptic transmission, cholinergic;response to nicotine;acetylcholine receptor signaling pathway;negative regulation of protein localization to plasma membrane;negative regulation of signaling receptor activity
• Cellular component: extracellular region;plasma membrane;anchored component of membrane
• Molecular function: acetylcholine receptor inhibitor activity;acetylcholine receptor binding