rs771126504
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002334.4(LRP4):c.3919C>T(p.Pro1307Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000124 in 1,613,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_002334.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRP4 | NM_002334.4 | c.3919C>T | p.Pro1307Ser | missense_variant | Exon 27 of 38 | ENST00000378623.6 | NP_002325.2 | |
LRP4 | XM_017017734.2 | c.3919C>T | p.Pro1307Ser | missense_variant | Exon 27 of 39 | XP_016873223.1 | ||
LRP4 | XM_011520103.3 | c.3115C>T | p.Pro1039Ser | missense_variant | Exon 21 of 32 | XP_011518405.1 | ||
LRP4 | XM_011520104.3 | c.1684C>T | p.Pro562Ser | missense_variant | Exon 12 of 23 | XP_011518406.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000639 AC: 16AN: 250336Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135440
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461592Hom.: 0 Cov.: 34 AF XY: 0.0000124 AC XY: 9AN XY: 727126
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74328
ClinVar
Submissions by phenotype
Cenani-Lenz syndactyly syndrome;C3280402:Sclerosteosis 2;C4225377:Congenital myasthenic syndrome 17 Uncertain:2
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This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 1307 of the LRP4 protein (p.Pro1307Ser). This variant is present in population databases (rs771126504, gnomAD 0.05%). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C25"). ClinVar contains an entry for this variant (Variation ID: 467788). This variant has not been reported in the literature in individuals affected with LRP4-related conditions. -
LRP4-related disorder Uncertain:1
The LRP4 c.3919C>T variant is predicted to result in the amino acid substitution p.Pro1307Ser. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.046% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/11-46897013-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at