rs1308485193
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP2PP3_Strong
The NM_002335.4(LRP5):āc.3242T>Cā(p.Leu1081Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,424 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L1081R) has been classified as Likely pathogenic.
Frequency
Consequence
NM_002335.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP5 | NM_002335.4 | c.3242T>C | p.Leu1081Pro | missense_variant | 15/23 | ENST00000294304.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP5 | ENST00000294304.12 | c.3242T>C | p.Leu1081Pro | missense_variant | 15/23 | 1 | NM_002335.4 | P1 | |
LRP5 | ENST00000529993.5 | c.*1848T>C | 3_prime_UTR_variant, NMD_transcript_variant | 15/23 | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249202Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134950
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461424Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727058
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at