rs387906884
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PP2PP3_StrongPP5
The NM_002334.4(LRP4):c.3508C>T(p.Arg1170Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,888 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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1170Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_002334.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP4 | NM_002334.4 | c.3508C>T | p.Arg1170Trp | missense_variant | 25/38 | ENST00000378623.6 | |
LRP4 | XM_017017734.2 | c.3508C>T | p.Arg1170Trp | missense_variant | 25/39 | ||
LRP4 | XM_011520103.3 | c.2704C>T | p.Arg902Trp | missense_variant | 19/32 | ||
LRP4 | XM_011520104.3 | c.1273C>T | p.Arg425Trp | missense_variant | 10/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP4 | ENST00000378623.6 | c.3508C>T | p.Arg1170Trp | missense_variant | 25/38 | 1 | NM_002334.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251232Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135770
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461888Hom.: 0 Cov.: 36 AF XY: 0.00000413 AC XY: 3AN XY: 727244
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Sclerosteosis 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at