LYPD6B

protein-coding

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

Gene summary

Enables acetylcholine receptor regulator activity. Predicted to be located in extracellular region and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_177964.5

Inheritance

—

ClinVar variants

U:26B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.6

Max pathogenic AF

—

Genomic locus

chr2:149,038,107-149,215,262

External References & Databases

Ensembl (ENSG00000150556)

Transcript & Mutation Effects

hg38 • Region Span ~177.2 kb

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GenCC 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 LYPD6B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 26

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_177964.5. 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 clinvar	1 clinvar		2
missense			23 clinvar	4 clinvar		27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	26	5	0	31

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 80 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_177964.5	RefSeq	NP_808879.2	6	MANE Select
ENST00000409642.8	Ensembl	ENSP00000387077.3	6	MANE Select
NM_001317002.2	RefSeq	NP_001303931.1	6	Standard
NM_001317003.2	RefSeq	NP_001303932.1	5	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
lypd6b	Danio rerio	Structure: inner ear Quality: lacks all parts of type abnormal

Gene / Model

Organism

Observed Phenotype

lypd6b

Danio rerio

Structure: inner ear

Quality: lacks all parts of type

abnormal

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

regulation of neurotransmitter receptor activity

Molecular Function

acetylcholine receptor regulator activity

Cellular Component

extracellular region
plasma membrane
anchored component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409642
Coding exons: 6
Length: 177156
Individuals with no LoFs: 124616
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 124638
p: 0.0000883

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.646	99	119	0.833	0.00000628	1372
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00019	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000071	rare
South Asian	0.00017	0.00016	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

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}.;

Intolerance Scores

RVIS EVS: -0.16
RVIS percentile EVS: 41.64

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.670

Gene Damage Prediction

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