LDLRAD3

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

Basic information

Region (hg38): 11:35943980-36232136

Links

ENSG00000179241 ∙ NCBI:143458 ∙ OMIM:617986 ∙ HGNC:27046 ∙ Uniprot:Q86YD5 ∙ 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 LDLRAD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LDLRAD3 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				2		2
missense			19	1	3	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	3	3

Variants in LDLRAD3

This is a list of pathogenic ClinVar variants found in the LDLRAD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-36036119-C-A			Likely benign (Dec 31, 2019)
11-36036159-T-G		not specified	Uncertain significance (Sep 06, 2022)
11-36036192-G-A			Benign (Dec 31, 2019)
11-36036240-A-G		not specified	Uncertain significance (Jun 29, 2023)
11-36081659-C-G		not specified	Uncertain significance (May 24, 2024)
11-36081722-G-A		not specified	Uncertain significance (Nov 21, 2023)
11-36081730-T-C		not specified	Uncertain significance (Aug 28, 2023)
11-36098353-G-A		not specified	Uncertain significance (Dec 21, 2023)
11-36098356-C-T		not specified	Uncertain significance (Apr 12, 2022)
11-36098374-G-A		not specified	Uncertain significance (Dec 22, 2023)
11-36098452-A-C			Likely benign (Dec 31, 2019)
11-36227087-C-T		not specified	Uncertain significance (Jan 18, 2023)
11-36227162-G-A		not specified	Uncertain significance (Jan 05, 2022)
11-36227252-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-36227273-G-A		not specified	Uncertain significance (Apr 07, 2022)
11-36227278-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
11-36227349-A-C		not specified	Uncertain significance (Aug 12, 2021)
11-36227355-T-A		not specified	Uncertain significance (Jan 24, 2024)
11-36227366-G-A		not specified	Uncertain significance (Aug 02, 2022)
11-36227367-C-T		not specified	Uncertain significance (Dec 17, 2023)
11-36229166-G-A			Likely benign (Apr 01, 2023)
11-36229175-C-G		not specified	Uncertain significance (Aug 30, 2022)
11-36229186-C-T		not specified	Uncertain significance (Jun 05, 2023)
11-36229224-G-T			Benign (Dec 31, 2019)
11-36229234-C-T		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LDLRAD3	protein_coding	protein_coding	ENST00000315571	6	288156

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0162	0.962	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.704	184	213	0.864	0.0000133	2280
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00199	0.00199
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.00	0.00
South Asian	0.000163	0.000163
Other	0.000165	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.271
• hipred: N
• hipred_score: 0.332
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.210

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ldlrad3

Gene ontology

• Biological process: receptor-mediated endocytosis;regulation of protein processing
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: amyloid-beta binding