LYPD1
protein-codingLY6/PLAUR domain containing 1, the group of LY6/PLAUR domain containing
Gene summary
Predicted to enable acetylcholine receptor inhibitor activity. Predicted to be involved in acetylcholine receptor signaling pathway. Predicted to act upstream of or within several processes, including behavioral fear response; cholinergic synaptic transmission; and negative regulation of protein localization to plasma membrane. Predicted to be located in extracellular region and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]
- LYPDC1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LYPD1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_144586.7. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 15 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 16 | 0 | 0 | 16 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_653187.3 | 3 | MANE Select | |
| Ensembl | ENSP00000380605.2 | 3 | MANE Select | |
| RefSeq | NP_001070895.1 | 2 | Standard | |
| RefSeq | NP_001308163.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Post-translational modification: synthesis of GPI-anchored proteins
- Post-translational protein modification
- Metabolism of proteins
Biological Process
- behavioral fear response
- synaptic transmission, cholinergic
- response to nicotine
- acetylcholine receptor signaling pathway
- negative regulation of protein localization to plasma membrane
Molecular Function
- acetylcholine receptor inhibitor activity
- acetylcholine receptor binding
Cellular Component
- extracellular region
- plasma membrane
- anchored component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000397463
- Coding exons
- 3
- Length
- 26727
- Individuals with no LoFs
- 124736
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 19
- Defined
- 124755
- p
- 0.0000762
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.498 | 63 | 75.1 | 0.838 | 0.00000390 | 912 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000066 | 0.000065 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000061 | 0.000056 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000063 | 0.000062 | rare |
| South Asian | 0.00025 | 0.00020 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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}.;
Intolerance Scores
- LoFtool
- 0.507
- RVIS EVS
- 0.3
- RVIS percentile EVS
- 72.01
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.231
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |