LDLRAD2
Basic information
Region (hg38): 1:21812264-21825225
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (112 variants)
- Lethal Kniest-like syndrome (58 variants)
- Schwartz-Jampel syndrome (56 variants)
- Inborn genetic diseases (34 variants)
- not specified (12 variants)
- Connective tissue disorder (8 variants)
- Schwartz-Jampel syndrome type 1 (4 variants)
- HSPG2-Related Disorders (1 variants)
- Microcephaly (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.
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 | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 79 | 51 | 13 | 146 | ||
| Total | 1 | 2 | 93 | 51 | 13 |
Highest pathogenic variant AF is 0.0000657
Variants in LDLRAD2
This is a list of pathogenic ClinVar variants found in the LDLRAD2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| 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:
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
- Phenotype
Gene ontology
- Biological process
- Cellular component
- integral component of membrane
- Molecular function