LYPD6
protein-codingLY6/PLAUR domain containing 6, the group of LY6/PLAUR domain containing
Gene summary
Members of the LY6 protein family (see SLURP1; MIM 606119), such as LYPD6, have at least one 80-amino acid LU domain that contains 10 conserved cysteines with a defined disulfide-bonding pattern (Zhang et al., 2010 [PubMed 19653121]).[supplied by OMIM, Apr 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~144.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: Unknown
Disease ID:MONDO:0007661
Submitter: Labcorp Genetics (formerly Invitae)
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LYPD6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_194317.5. 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 | 1 | 1 | 2 | |||
| missense | 20 | 20 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 21 | 0 | 1 | 22 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_919298.1 | 4 | MANE Select | |
| Ensembl | ENSP00000334463.4 | 4 | MANE Select | |
| RefSeq | NP_001182614.1 | 4 | Standard | |
| Ensembl | ENSP00000376594.4 | 3 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| lypd6 | Danio rerio | Structure: trunk Quality: decreased size abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of neurotransmitter receptor activity
- negative regulation of signaling receptor activity
Molecular Function
- protein binding
- acetylcholine receptor inhibitor activity
Cellular Component
- extracellular region
- cytoplasm
- plasma membrane
- cell junction
- anchored component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000334166
- Coding exons
- 4
- Length
- 144164
- Individuals with no LoFs
- 125636
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 94
- Defined
- 125730
- p
- 0.000374
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.330 | 87 | 96.1 | 0.905 | 0.00000505 | 1090 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.0018 | 0.0018 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00018 | 0.00018 | rare |
| South Asian | 0.000099 | 0.000098 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- 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
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |