rs34291900

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

Scores

6
7
5

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 7.79
Variant links:
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]

Genome browser will be placed here

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
LRP2NM_004525.3 linkuse as main transcriptc.2006G>A p.Gly669Asp missense_variant 15/79 ENST00000649046.1 NP_004516.2 P98164Q7Z5C0Q7Z5C1
LRP2XM_011511183.4 linkuse as main transcriptc.2006G>A p.Gly669Asp missense_variant 15/78 XP_011509485.1
LRP2XM_047444340.1 linkuse as main transcriptc.1082G>A p.Gly361Asp missense_variant 15/79 XP_047300296.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LRP2ENST00000649046.1 linkuse as main transcriptc.2006G>A p.Gly669Asp missense_variant 15/79 NM_004525.3 ENSP00000496870.1 P98164
LRP2ENST00000443831.1 linkuse as main transcriptc.1799G>A p.Gly600Asp missense_variant 14/232 ENSP00000409813.1 E9PC35
LRP2ENST00000493501.1 linkuse as main transcriptn.349G>A non_coding_transcript_exon_variant 2/34

Frequencies

GnomAD3 genomes
AF:
0.0249
AC:
3790
AN:
152142
Hom.:
62
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.00572
Gnomad AMI
AF:
0.0505
Gnomad AMR
AF:
0.0202
Gnomad ASJ
AF:
0.0222
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.0274
Gnomad FIN
AF:
0.0455
Gnomad MID
AF:
0.0191
Gnomad NFE
AF:
0.0362
Gnomad OTH
AF:
0.0177
GnomAD3 exomes
AF:
0.0280
AC:
7012
AN:
250820
Hom.:
140
AF XY:
0.0294
AC XY:
3979
AN XY:
135514
show subpopulations
Gnomad AFR exome
AF:
0.00566
Gnomad AMR exome
AF:
0.0133
Gnomad ASJ exome
AF:
0.0264
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.0341
Gnomad FIN exome
AF:
0.0447
Gnomad NFE exome
AF:
0.0352
Gnomad OTH exome
AF:
0.0317
GnomAD4 exome
AF:
0.0343
AC:
50082
AN:
1461280
Hom.:
978
Cov.:
37
AF XY:
0.0345
AC XY:
25046
AN XY:
726948
show subpopulations
Gnomad4 AFR exome
AF:
0.00484
Gnomad4 AMR exome
AF:
0.0143
Gnomad4 ASJ exome
AF:
0.0232
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.0340
Gnomad4 FIN exome
AF:
0.0431
Gnomad4 NFE exome
AF:
0.0373
Gnomad4 OTH exome
AF:
0.0304
GnomAD4 genome
AF:
0.0249
AC:
3787
AN:
152260
Hom.:
62
Cov.:
34
AF XY:
0.0255
AC XY:
1895
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.00570
Gnomad4 AMR
AF:
0.0202
Gnomad4 ASJ
AF:
0.0222
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0274
Gnomad4 FIN
AF:
0.0455
Gnomad4 NFE
AF:
0.0362
Gnomad4 OTH
AF:
0.0175
Alfa
AF:
0.0317
Hom.:
129
Bravo
AF:
0.0217
TwinsUK
AF:
0.0421
AC:
156
ALSPAC
AF:
0.0368
AC:
142
ESP6500AA
AF:
0.00567
AC:
25
ESP6500EA
AF:
0.0352
AC:
303
ExAC
AF:
0.0285
AC:
3457
Asia WGS
AF:
0.00924
AC:
32
AN:
3478
EpiCase
AF:
0.0354
EpiControl
AF:
0.0336

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 providedclinical testingGenetic 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 submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpDec 10, 2021- -
Benign, criteria provided, single submitterclinical testingGenomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of PhiladelphiaAug 19, 2015- -
Likely benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
not provided Benign:3
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024- -
Benign, criteria provided, single submitterclinical testingGeneDxDec 28, 2020This variant is associated with the following publications: (PMID: 21303902) -
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Donnai-Barrow syndrome Benign:2
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaMar 06, 2018This 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 submitterclinical testingGenome-Nilou LabJul 15, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Uncertain
0.090
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.36
T;T;T
Eigen
Pathogenic
0.87
Eigen_PC
Pathogenic
0.83
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.89
.;D;T
MetaRNN
Benign
0.012
T;T;T
MetaSVM
Uncertain
0.21
D
MutationAssessor
Uncertain
2.7
M;M;.
PrimateAI
Uncertain
0.56
T
PROVEAN
Pathogenic
-5.4
.;D;D
REVEL
Pathogenic
0.65
Sift
Uncertain
0.0010
.;D;D
Sift4G
Pathogenic
0.0010
.;D;D
Polyphen
1.0
D;D;D
Vest4
0.86, 0.33
MPC
1.0
ClinPred
0.019
T
GERP RS
5.4
Varity_R
0.91
gMVP
0.76

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs34291900; hg19: chr2-170129547; COSMIC: COSV104378672; API