Variant #0000091351 (NC_000019.9:g.11200086C>G, LDLR(NM_000527.4):c.-139C>G)

Individual ID 00060342
Chromosome 19
Allele Parent #1
Affects function (as reported) Probably affects function
Affects function (by curator) Probably affects function
Classification method ACGS
Clinical classification likely pathogenic
DNA change (genomic) (Relative to hg19 / GRCh37) g.11200086C>G
DNA change (hg38) g.11089410C>G
Published as -
ISCN -
DB-ID LDLR_001190 See all 2 reported entries
Variant remarks predicted reduced transcription; Proband compound Htz with c.762_763inv, p.(Q254_C255delinsHG), inherited from mother & c.-22delC from father; Not found in 50 normals; Creates new initiation site, which could result in an novel peptide of 35aa.
Reference PubMed: Smith 2007
ClinVar ID -
dbSNP ID -
Origin Germline
Segregation -
Frequency -
Re-site -
VIP 0
Methylation -
Average frequency (gnomAD v.2.1.1) Variant not found in online data sets
Owner Sarah Leigh
Database submission license Creative Commons Attribution-NonCommercial-ShareAlike 4.0 InternationalCreative Commons License
Created by Johan den Dunnen
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Variant on transcripts


Gene     

AscendingTranscript     

Affects function     

Exon     

DNA change (cDNA)     

RNA change     

Protein     

Predict/MutationTaster     

P-domain     

Predict/PolyPhen     

Predict/SIFT     

Conservation     

Predict/Splice     

Enzyme activity     
LDLR NM_000527.4 +?/+? 1 c.-139C>G r.(=) p.(=) - SP1 binding site - - 13/13 conservation {PMID25248394:Khamis et al European Journal of Human Genetics (2015) 23, 790–795} - 26% of wt using luciferase assay



Screenings


AscendingScreening ID     

Template     

Technique     

Tissue     

Remarks     

Genes screened     

Variants found     

Owner     
0000060331 DNA SSCA - - LDLR 1 Sarah Leigh