rs34355135

Variant names:

• chr2-169173147-C-G
• NM_004525.3:c.11092G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-169173147-C-G
• chr2-169173147-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_004525.3(LRP2):​c.11092G>C​(p.Val3698Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign 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. V3698M) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LRP2 NM_004525.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.28750846).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRP2	NM_004525.3	c.11092G>C	p.Val3698Leu	missense_variant	Exon 57 of 79	ENST00000649046.1	NP_004516.2
LRP2	XM_047444340.1	c.10168G>C	p.Val3390Leu	missense_variant	Exon 57 of 79		XP_047300296.1
LRP2	XM_011511184.3	c.8803G>C	p.Val2935Leu	missense_variant	Exon 42 of 64		XP_011509486.1
LRP2	XM_011511183.4	c.11014+772G>C		intron_variant	Intron 56 of 77		XP_011509485.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRP2	ENST00000649046.1	c.11092G>C	p.Val3698Leu	missense_variant	Exon 57 of 79		NM_004525.3	ENSP00000496870.1
LRP2	ENST00000649153.1	n.1990G>C		non_coding_transcript_exon_variant	Exon 9 of 30			ENSP00000497617.1
LRP2	ENST00000650252.1	n.124G>C		non_coding_transcript_exon_variant	Exon 2 of 24			ENSP00000496887.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Uncertain	0.015	T
BayesDel_noAF	Benign	-0.22
CADD	Benign	3.1
DANN	Benign	0.61
DEOGEN2	Benign	0.20	T;T
Eigen	Benign	-0.92
Eigen_PC	Benign	-0.95
FATHMM_MKL	Benign	0.74	D
LIST_S2	Benign	0.18	.;T
M_CAP	Benign	0.063	D
MetaRNN	Benign	0.29	T;T
MetaSVM	Uncertain	-0.23	T
MutationAssessor	Benign	0.74	N;N
PrimateAI	Benign	0.27	T
PROVEAN	Benign	-0.81	.;N
REVEL	Uncertain	0.35
Sift	Benign	0.46	.;T
Sift4G	Uncertain	0.012	.;D
Polyphen		0.41	B;B
Vest4		0.30
MutPred		0.53		Gain of catalytic residue at V3698 (P = 0.0687);Gain of catalytic residue at V3698 (P = 0.0687);
MVP		0.47
MPC		0.26
ClinPred		0.43	T
GERP RS		-0.88
Varity_R		0.054
gMVP		0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-170029657;