NM_003667.4:c.1063C>G

Variant names:

• chr12-71566905-C-G
• NM_003667.4:c.1063C>G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_003667.4(LGR5):​c.1063C>G​(p.Gln355Glu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: LGR5 NM_003667.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.92

Genes affected

LGR5 (HGNC:4504): (leucine rich repeat containing G protein-coupled receptor 5) The protein encoded by this gene is a leucine-rich repeat-containing receptor (LGR) and member of the G protein-coupled, 7-transmembrane receptor (GPCR) superfamily. The encoded protein is a receptor for R-spondins and is involved in the canonical Wnt signaling pathway. This protein plays a role in the formation and maintenance of adult intestinal stem cells during postembryonic development. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]

LOC105369833 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LGR5	NM_003667.4	c.1063C>G	p.Gln355Glu	missense_variant	Exon 11 of 18	ENST00000266674.10	NP_003658.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LGR5	ENST00000266674.10	c.1063C>G	p.Gln355Glu	missense_variant	Exon 11 of 18	1	NM_003667.4	ENSP00000266674.4
LGR5	ENST00000540815.2	c.991C>G	p.Gln331Glu	missense_variant	Exon 10 of 17	1		ENSP00000441035.2
LGR5	ENST00000536515.5	c.847C>G	p.Gln283Glu	missense_variant	Exon 10 of 17	1		ENSP00000443033.1
LGR5	ENST00000550851.5	n.1160C>G		non_coding_transcript_exon_variant	Exon 11 of 20	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Dec 12, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1063C>G (p.Q355E) alteration is located in exon 11 (coding exon 11) of the LGR5 gene. This alteration results from a C to G substitution at nucleotide position 1063, causing the glutamine (Q) at amino acid position 355 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.086
BayesDel_addAF	Benign	-0.019	T
BayesDel_noAF	Benign	-0.26
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.12	T;.;.
Eigen	Benign	-0.048
Eigen_PC	Benign	0.20
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.79	T;T;T
M_CAP	Benign	0.0075	T
MetaRNN	Uncertain	0.54	D;D;D
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	0.49	N;.;.
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-1.6	N;N;N
REVEL	Benign	0.19
Sift	Benign	0.038	D;D;D
Sift4G	Uncertain	0.018	D;T;D
Polyphen		0.22	B;.;B
Vest4		0.69
MutPred		0.37		Gain of sheet (P = 0.1208);.;.;
MVP		0.72
MPC		0.18
ClinPred		0.85	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.33
gMVP		0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: chr12-71960685;