LDLRAD4

low density lipoprotein receptor class A domain containing 4, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 18:13217498-13652755

Previous symbols: [ "C18orf1" ]

Links

ENSG00000168675 ∙ NCBI:753 ∙ OMIM:606571 ∙ HGNC:1224 ∙ Uniprot:O15165 ∙ 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 LDLRAD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LDLRAD4 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in LDLRAD4

This is a list of pathogenic ClinVar variants found in the LDLRAD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-13438289-C-T		not specified	Uncertain significance (Dec 17, 2023)
18-13621128-T-C		not specified	Uncertain significance (Jul 11, 2023)
18-13621231-G-A			Likely benign (Jan 01, 2023)
18-13621234-C-T		not specified	Uncertain significance (Sep 23, 2023)
18-13621246-G-A		not specified	Uncertain significance (Jan 09, 2024)
18-13621267-C-T		not specified	Uncertain significance (May 10, 2022)
18-13643386-G-A		not specified	Uncertain significance (May 31, 2024)
18-13643402-G-A		not specified	Uncertain significance (Jul 25, 2023)
18-13643408-C-T		not specified	Uncertain significance (Dec 16, 2022)
18-13645143-G-A		not specified	Uncertain significance (Jul 20, 2021)
18-13645187-C-T		not specified	Uncertain significance (May 24, 2023)
18-13645227-A-G		not specified	Uncertain significance (Oct 26, 2022)
18-13645436-A-T		not specified	Uncertain significance (Apr 05, 2023)
18-13645473-G-A		not specified	Uncertain significance (Jun 10, 2024)
18-13645503-G-T		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LDLRAD4	protein_coding	protein_coding	ENST00000361205	5	435258

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.620	0.378	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	137	200	0.686	0.0000128	2019
Missense in Polyphen		44	83.369	0.52778		846
Synonymous	-0.189	88	85.8	1.03	0.00000631	603
Loss of Function	2.63	2	11.7	0.171	6.71e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a negative regulator of TGF-beta signaling and thereby probably plays a role in cell proliferation, differentiation, apoptosis, motility, extracellular matrix production and immunosuppression. In the canonical TGF-beta pathway, ZFYVE9/SARA recruits the intracellular signal transducer and transcriptional modulators SMAD2 and SMAD3 to the TGF-beta receptor. Phosphorylated by the receptor, SMAD2 and SMAD3 then form a heteromeric complex with SMAD4 that translocates to the nucleus to regulate transcription. Through interaction with SMAD2 and SMAD3, LDLRAD4 may compete with ZFYVE9 and SMAD4 and prevent propagation of the intracellular signal. {ECO:0000269|PubMed:24627487}.

Recessive Scores

• pRec: 0.0990

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.539
• hipred: Y
• hipred_score: 0.692
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ldlrad4
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: negative regulation of epithelial to mesenchymal transition;negative regulation of SMAD protein complex assembly;negative regulation of cell migration;negative regulation of transforming growth factor beta receptor signaling pathway;negative regulation of pathway-restricted SMAD protein phosphorylation
• Cellular component: nucleoplasm;integral component of membrane;early endosome membrane;intracellular membrane-bounded organelle
• Molecular function: R-SMAD binding