rs34291900
Positions:
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_004525.3(LRP2):c.2006G>A(p.Gly669Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0334 in 1,613,540 control chromosomes in the GnomAD database, including 1,040 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.025 ( 62 hom., cov: 34)
Exomes 𝑓: 0.034 ( 978 hom. )
Consequence
LRP2
NM_004525.3 missense
NM_004525.3 missense
Scores
6
7
5
Clinical Significance
Conservation
PhyloP100: 7.79
Genes affected
LRP2 (HGNC:6694): (LDL receptor related protein 2) The protein encoded by this gene, low density lipoprotein-related protein 2 (LRP2) or megalin, is a multi-ligand endocytic receptor that is expressed in many different tissues but primarily in absorptive epithilial tissues such as the kidney. This glycoprotein has a large amino-terminal extracellular domain, a single transmembrane domain, and a short carboxy-terminal cytoplasmic tail. The extracellular ligand-binding-domains bind diverse macromolecules including albumin, apolipoproteins B and E, and lipoprotein lipase. The LRP2 protein is critical for the reuptake of numerous ligands, including lipoproteins, sterols, vitamin-binding proteins, and hormones. This protein also has a role in cell-signaling; extracellular ligands include parathyroid horomones and the morphogen sonic hedgehog while cytosolic ligands include MAP kinase scaffold proteins and JNK interacting proteins. Recycling of this membrane receptor is regulated by phosphorylation of its cytoplasmic domain. Mutations in this gene cause Donnai-Barrow syndrome (DBS) and facio-oculoacoustico-renal syndrome (FOAR).[provided by RefSeq, Aug 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), LRP2. . Trascript score misZ 4.5094 (greater than threshold 3.09). GenCC has associacion of gene with intellectual disability, autosomal dominant 40, Stickler syndrome, Donnai-Barrow syndrome.
BP4
Computational evidence support a benign effect (MetaRNN=0.012386203).
BP6
Variant 2-169273037-C-T is Benign according to our data. Variant chr2-169273037-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 129506.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-169273037-C-T is described in Lovd as [Benign]. Variant chr2-169273037-C-T is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0249 (3787/152260) while in subpopulation NFE AF= 0.0362 (2460/68026). AF 95% confidence interval is 0.035. There are 62 homozygotes in gnomad4. There are 1895 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 62 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRP2 | NM_004525.3 | c.2006G>A | p.Gly669Asp | missense_variant | 15/79 | ENST00000649046.1 | NP_004516.2 | |
LRP2 | XM_011511183.4 | c.2006G>A | p.Gly669Asp | missense_variant | 15/78 | XP_011509485.1 | ||
LRP2 | XM_047444340.1 | c.1082G>A | p.Gly361Asp | missense_variant | 15/79 | XP_047300296.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRP2 | ENST00000649046.1 | c.2006G>A | p.Gly669Asp | missense_variant | 15/79 | NM_004525.3 | ENSP00000496870.1 | |||
LRP2 | ENST00000443831.1 | c.1799G>A | p.Gly600Asp | missense_variant | 14/23 | 2 | ENSP00000409813.1 | |||
LRP2 | ENST00000493501.1 | n.349G>A | non_coding_transcript_exon_variant | 2/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0249 AC: 3790AN: 152142Hom.: 62 Cov.: 34
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0280 AC: 7012AN: 250820Hom.: 140 AF XY: 0.0294 AC XY: 3979AN XY: 135514
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GnomAD4 exome AF: 0.0343 AC: 50082AN: 1461280Hom.: 978 Cov.: 37 AF XY: 0.0345 AC XY: 25046AN XY: 726948
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GnomAD4 genome AF: 0.0249 AC: 3787AN: 152260Hom.: 62 Cov.: 34 AF XY: 0.0255 AC XY: 1895AN XY: 74422
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TwinsUK
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156
ALSPAC
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142
ESP6500AA
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25
ESP6500EA
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Asia WGS
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:9
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:4
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Aug 19, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 28, 2020 | This variant is associated with the following publications: (PMID: 21303902) - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Donnai-Barrow syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;D;T
MetaRNN
Benign
T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M;.
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
.;D;D
REVEL
Pathogenic
Sift
Uncertain
.;D;D
Sift4G
Pathogenic
.;D;D
Polyphen
D;D;D
Vest4
0.86, 0.33
MPC
1.0
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at