LYPD6B

LY6/PLAUR domain containing 6B, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 2:149038107-149215262

Links

ENSG00000150556 ∙ NCBI:130576 ∙ ∙ HGNC:27018 ∙ Uniprot:Q8NI32 ∙ 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 LYPD6B gene.

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.

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			11	3		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	3	0

Variants in LYPD6B

This is a list of pathogenic ClinVar variants found in the LYPD6B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-149160783-A-G		not specified	Likely benign (May 18, 2022)
2-149205278-C-T		not specified	Uncertain significance (May 18, 2022)
2-149205288-G-A		not specified	Uncertain significance (May 18, 2023)
2-149205308-G-A		not specified	Likely benign (Jul 12, 2023)
2-149205308-G-T		not specified	Uncertain significance (Feb 11, 2022)
2-149205311-C-G		not specified	Uncertain significance (May 20, 2024)
2-149205314-G-A		not specified	Uncertain significance (Oct 10, 2023)
2-149208338-A-G		not specified	Uncertain significance (Oct 25, 2023)
2-149208380-A-G		not specified	Uncertain significance (Jul 26, 2022)
2-149213034-G-T		not specified	Uncertain significance (Mar 06, 2023)
2-149213039-A-C		not specified	Uncertain significance (Aug 21, 2023)
2-149214558-T-G		not specified	Uncertain significance (Jun 22, 2024)
2-149214562-G-A		not specified	Uncertain significance (Aug 13, 2021)
2-149214579-A-G			Uncertain significance (Feb 01, 2024)
2-149214621-G-A		not specified	Likely benign (May 04, 2022)
2-149214672-C-T		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• 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