LDLRAD2

low density lipoprotein receptor class A domain containing 2

Basic information

Region (hg38): 1:21812265-21825225

Links

ENSG00000187942 ∙ NCBI:401944 ∙ ∙ HGNC:32071 ∙ Uniprot:Q5SZI1 ∙ 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 LDLRAD2 gene.

• not_specified (46 variants)
• Schwartz-Jampel_syndrome_type_1 (2 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LDLRAD2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001013693.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			45	1		46
nonsense						0
start loss						0
frameshift	1					1
splice donor/acceptor (+/-2bp)						0
Total	1	0	45	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LDLRAD2	protein_coding	protein_coding	ENST00000344642	5	12957

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000214	0.753	125703	0	42	125745	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.192	161	154	1.04	0.00000784	1680
Missense in Polyphen		37	36.937	1.0017		452
Synonymous	-0.651	81	73.9	1.10	0.00000392	611
Loss of Function	1.02	7	10.6	0.662	4.53e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.000167	0.000163
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000150	0.000132
Middle Eastern	0.000167	0.000163
South Asian	0.000557	0.000555
Other	0.000177	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.462
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.280
• hipred: N
• hipred_score: 0.208
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0199

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ldlrad2

Gene ontology

• Cellular component: integral component of membrane