LDLRAD1

low density lipoprotein receptor class A domain containing 1

Basic information

Region (hg38): 1:54007298-54018186

Links

ENSG00000203985 ∙ NCBI:388633 ∙ ∙ HGNC:32069 ∙ Uniprot:Q5T700 ∙ 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 LDLRAD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LDLRAD1 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			10	4		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	10	4	0

Variants in LDLRAD1

This is a list of pathogenic ClinVar variants found in the LDLRAD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-54009003-C-G		not specified	Uncertain significance (Jan 19, 2024)
1-54009040-C-T		not specified	Uncertain significance (Jun 22, 2024)
1-54009046-A-G		not specified	Uncertain significance (Sep 12, 2023)
1-54009086-A-G		not specified	Likely benign (Nov 09, 2021)
1-54009094-C-T		not specified	Likely benign (Jun 17, 2022)
1-54009115-G-C		not specified	Uncertain significance (Mar 29, 2024)
1-54010284-G-A		not specified	Uncertain significance (Apr 08, 2022)
1-54010309-C-T		not specified	Uncertain significance (Jun 28, 2023)
1-54010311-C-T		not specified	Uncertain significance (Nov 15, 2023)
1-54010320-G-A		not specified	Likely benign (Oct 27, 2023)
1-54012251-T-C		not specified	Uncertain significance (Apr 23, 2024)
1-54014304-A-C		not specified	Uncertain significance (Aug 17, 2021)
1-54014356-C-T		not specified	Likely benign (Dec 28, 2023)
1-54017417-C-A		not specified	Uncertain significance (Feb 15, 2023)
1-54018097-G-A		not specified	Uncertain significance (May 03, 2023)
1-54018097-G-C		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LDLRAD1	protein_coding	protein_coding	ENST00000371360	6	9445

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000123	0.377	125316	3	426	125745	0.00171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.279	120	129	0.931	0.00000760	1312
Missense in Polyphen		46	46.389	0.99161		529
Synonymous	0.133	54	55.3	0.977	0.00000379	400
Loss of Function	0.502	10	11.9	0.843	6.89e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0228	0.0227
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000980	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.364
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.209

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ldlrad1

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding