LYPD3

protein-coding

LY6/PLAUR domain containing 3, the group of LY6/PLAUR domain containing

Gene summary

Predicted to enable laminin binding activity. Involved in negative regulation of smooth muscle cell apoptotic process. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_014400.3

Inheritance

—

ClinVar variants

U:53B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.43

Max pathogenic AF

—

Genomic locus

chr19:43,460,787-43,465,608

External References & Databases

Ensembl (ENSG00000124466)

Transcript & Mutation Effects

hg38 • Region Span ~4.8 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 LYPD3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 51

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014400.3. 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			2 clinvar		2 clinvar	4
missense			49 clinvar	2 clinvar	1 clinvar	52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	53	2	3	58

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014400.3	RefSeq	NP_055215.2	5	MANE Select
ENST00000244333.4	Ensembl	ENSP00000244333.2	5	MANE Select

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

cell-matrix adhesion

Molecular Function

laminin binding

Cellular Component

extracellular region
extracellular space
plasma membrane
integral component of membrane
anchored component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000244333
Coding exons: 5
Length: 4874
Individuals with no LoFs: 125653
Homozygous LoFs: 1
Heterozygous LoFs: 90
Defined: 125744
p: 0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0820	206	209	0.984	0.0000117	2169
Missense (PolyPhen)		73	75.605	0.96554		826
Synonymous	0.527	86	92.4	0.930	0.00000512	764
Loss of Function	-1.25	14	9.78	1.43	4.20e-7	105

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00052	0.00052	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00048	0.00046	rare
South Asian	0.00040	0.00039	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Supports cell migration. May be involved in urothelial cell-matrix interactions. May be involved in tumor progression. {ECO:0000269|PubMed:11179665, ECO:0000269|PubMed:11245483, ECO:0000269|PubMed:12592373, ECO:0000269|PubMed:15012588}.;

Recessive Scores

pRec: 0.126

Intolerance Scores

LoFtool: 0.796
RVIS EVS: 0.02
RVIS percentile EVS: 55.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.450

Gene Damage Prediction

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