LDLRAD3

protein-coding

low density lipoprotein receptor class A domain containing 3, the group of MicroRNA protein coding host genes

Gene summary

Predicted to enable amyloid-beta binding activity. Predicted to be involved in receptor-mediated endocytosis. Predicted to act upstream of or within regulation of protein processing. Predicted to be located in endomembrane system and membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_174902.4

Inheritance

—

ClinVar variants

U:46B:7

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr11:35,943,981-36,232,136

External References & Databases

Ensembl (ENSG00000179241)

Transcript & Mutation Effects

hg38 • Region Span ~288.2 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 LDLRAD3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 6

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174902.4. 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				3 clinvar		3
missense			44 clinvar	1 clinvar	3 clinvar	48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	46	4	3	53

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174902.4	RefSeq	NP_777562.1	6	MANE Select
ENST00000315571.6	Ensembl	ENSP00000318607.5	6	MANE Select
NM_001304263.2	RefSeq	NP_001291192.1	5	Standard
NM_001304264.2	RefSeq	NP_001291193.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

receptor-mediated endocytosis
regulation of protein processing

Molecular Function

amyloid-beta binding

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000315571
Coding exons: 6
Length: 288156
Individuals with no LoFs: 125677
Homozygous LoFs: 0
Heterozygous LoFs: 71
Defined: 125748
p: 0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.704	184	213	0.864	0.0000133	2280
Missense (PolyPhen)		71	86.882	0.8172		853
Synonymous	1.55	76	95.2	0.798	0.00000676	682
Loss of Function	2.00	5	12.7	0.394	6.37e-7	150

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.0020	0.0020	notable
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00016	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May influence APP processing, resulting in a decrease in sAPP-alpha production and increased amyloidogenic P3 peptide production. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.195
RVIS EVS: -0.2
RVIS percentile EVS: 38.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.210

Gene Damage Prediction

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