rs80358305
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP2PP3_StrongPP5
The NM_002335.4(LRP5):c.433C>T(p.Leu145Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,300 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. L145L) has been classified as Likely benign.
Frequency
Consequence
NM_002335.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP5 | NM_002335.4 | c.433C>T | p.Leu145Phe | missense_variant | 2/23 | ENST00000294304.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP5 | ENST00000294304.12 | c.433C>T | p.Leu145Phe | missense_variant | 2/23 | 1 | NM_002335.4 | P1 | |
LRP5 | ENST00000529993.5 | c.433C>T | p.Leu145Phe | missense_variant, NMD_transcript_variant | 2/23 | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460300Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726564
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Osteoporosis with pseudoglioma Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2010 | - - |
Exudative vitreoretinopathy 4, autosomal dominant Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2010 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at