LYPD6B
Basic information
Region (hg38): 2:149038107-149215262
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (24 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYPD6B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000177964.5. 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 | |||||
| missense | 21 | 24 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 21 | 4 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LYPD6B | protein_coding | protein_coding | ENST00000409642 | 6 | 177156 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000361 | 0.845 | 124616 | 0 | 22 | 124638 | 0.0000883 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.646 | 99 | 119 | 0.833 | 0.00000628 | 1372 |
| Missense in Polyphen | 38 | 46.662 | 0.81437 | 533 | ||
| Synonymous | -0.343 | 48 | 45.1 | 1.06 | 0.00000278 | 382 |
| Loss of Function | 1.27 | 7 | 11.7 | 0.600 | 7.46e-7 | 119 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000310 | 0.000310 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000556 | 0.0000556 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000710 | 0.0000708 |
| Middle Eastern | 0.0000556 | 0.0000556 |
| South Asian | 0.000166 | 0.000163 |
| Other | 0.000165 | 0.000165 |
dbNSFP
Source:
- Function
- FUNCTION: Believed to act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro acts on nAChRs in a subtype- and stoichiometry-dependent manner. Modulates specifically alpha-3(3):beta-4(2) nAChRs by enhancing the sensitivity to ACh, decreasing ACh-induced maximal current response and increasing the rate of desensitization to ACh; has no effect on alpha-7 homomeric nAChRs; modulates alpha-3(2):alpha- 5:beta-4(2) nAChRs in the context of CHRNA5/alpha-5 variant Asn- 398 but not its wild-type sequence. {ECO:0000269|PubMed:26586467}.;
- Pathway
- Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.64
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.123
- ghis
- 0.561
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.670
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lypd6b
- Phenotype
- skeleton phenotype; limbs/digits/tail phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- lypd6b
- Affected structure
- inner ear
- Phenotype tag
- abnormal
- Phenotype quality
- lacks all parts of type
Gene ontology
- Biological process
- regulation of neurotransmitter receptor activity
- Cellular component
- extracellular region;plasma membrane;anchored component of membrane
- Molecular function
- acetylcholine receptor regulator activity