19-11102699-G-T

Variant names:

• chr19-11102699-G-T
• rs574337291
• NM_000527.5:c.226G>T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 7P and 4B. PP1_Moderate PM2 BS3 PS4_Supporting PP3 PP4

This summary comes from the ClinGen Evidence Repository: The NM_000527.5(LDLR):c.226G>T (p.Gly76Trp) variant is classified as Uncertain significance - conflicting evidence for Familial Hypercholesterolemia by applying evidence codes BS3, PS4_Supporting, PM2, PP1_Moderate, and PP4 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: BS3: Level 1 assays: PMID 25741862: Heterologous cells (CHO), western blot and flow cytometry assays - result: 100% low-density lipoprotein particle receptor biosynthetic process; 90% low-density lipoprotein particle binding; 95% low-density lipoprotein particle clearance. ---- The whole cycle is above 90% of wild-type activity. So, BS3 is met. PS4_Supporting: Variant meets PM2 and is identified in 2 index cases (1 case with DLCN criteria of definite FH from U4M - Lille University & CHRU Lille and 1 case with Simon Broome criteria of possible FH from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge). So, PS4_Supporting is met. PM2: This variant is absent from gnomAD (gnomAD v2.1.1). So, PM2 is met. PP3: REVEL=0.898. It is above 0.75, so PP3 is met. PP1_Moderate: Variant segregates with FH phenotype in 4 informative meioses in 1 family from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge. So, PP1_Moderate is met. PP4: Variant meets PM2 and is identified in 2 unrelated index cases who fulfill clinical criteria for FH from different labs, after alternative causes of high cholesterol were excluded (see PS4 for details). So, PP4 is met. LINK:https://erepo.genome.network/evrepo/ui/classification/CA10584797/MONDO:0007750/013

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.000012 (0 hom.)
• Consequence: LDLR NM_000527.5 missense
• Clinical Significance: Uncertain significance reviewed by expert panel P:2 U:6 B:3
• Conservation: PhyloP100: 8.02

Genes affected

LDLR (HGNC:6547): (low density lipoprotein receptor) The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. The encoded protein is normally bound at the cell membrane, where it binds low density lipoprotein/cholesterol and is taken into the cell. Lysosomes release the cholesterol, which is made available for repression of microsomal enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase, the rate-limiting step in cholesterol synthesis. At the same time, a reciprocal stimulation of cholesterol ester synthesis takes place. Mutations in this gene cause the autosomal dominant disorder, familial hypercholesterolemia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PS4: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PP1: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.
• BS3: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LDLR	NM_000527.5	c.226G>T	p.Gly76Trp	missense_variant	Exon 3 of 18	ENST00000558518.6	NP_000518.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LDLR	ENST00000558518.6	c.226G>T	p.Gly76Trp	missense_variant	Exon 3 of 18	1	NM_000527.5	ENSP00000454071.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.0000123 AC: 18 AN: 1461652 Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7 AN XY: 727134

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000153

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 31

Bravo AF: 0.00000756

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:2 Uncertain:6 Benign:3

Revision: reviewed by expert panel

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:2 Uncertain:2 Benign:2

Dec 16, 2016

Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

subject mutated among 2600 FH index cases screened = 1 , family member = 1 with co-segregation / mild phenotype / Software predictions: Damaging -

Mar 25, 2016

LDLR-LOVD, British Heart Foundation

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: literature only

- -

Mar 30, 2017

U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 28, 2023

ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel

Significance: Uncertain significance

Review Status: reviewed by expert panel

Collection Method: curation

The NM_000527.5(LDLR):c.226G>T (p.Gly76Trp) variant is classified as Uncertain significance - conflicting evidence for Familial Hypercholesterolemia by applying evidence codes BS3, PS4_Supporting, PM2, PP1_Moderate, and PP4 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: BS3: Level 1 assays: PMID 25741862: Heterologous cells (CHO), western blot and flow cytometry assays - result: 100% low-density lipoprotein particle receptor biosynthetic process; 90% low-density lipoprotein particle binding; 95% low-density lipoprotein particle clearance. ---- The whole cycle is above 90% of wild-type activity. So, BS3 is met. PS4_Supporting: Variant meets PM2 and is identified in 2 index cases (1 case with DLCN criteria of definite FH from U4M - Lille University & CHRU Lille and 1 case with Simon Broome criteria of possible FH from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge). So, PS4_Supporting is met. PM2: This variant is absent from gnomAD (gnomAD v2.1.1). So, PM2 is met. PP3: REVEL=0.898. It is above 0.75, so PP3 is met. PP1_Moderate: Variant segregates with FH phenotype in 4 informative meioses in 1 family from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge. So, PP1_Moderate is met. PP4: Variant meets PM2 and is identified in 2 unrelated index cases who fulfill clinical criteria for FH from different labs, after alternative causes of high cholesterol were excluded (see PS4 for details). So, PP4 is met. -

Feb 24, 2023

All of Us Research Program, National Institutes of Health

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 01, 2016

Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: research

0/100 normolipidemic individuals -

Familial hypercholesterolemia Uncertain:1 Benign:1

Jan 22, 2020

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: curation

The p.Gly76Trp variant in LDLR has been reported in at least 1 Portuguese individual with familial hypercholesterolemia (PMID: 17765246), and was absent from large population studies. This variant has also been reported in ClinVar as having conflicting interpretations of pathogenicity (Variation ID: rs574337291). In vitro functional studies provide some evidence that the p.Gly76Trp variant may not impact protein function (PMID: 25741862). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, the clinical significance of the p.Gly76Trp variant is uncertain. ACMG/AMP Criteria applied: PM2, PP3, BS3_supporting (Richards 2015). -

May 15, 2017

Color Diagnostics, LLC DBA Color Health

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Uncertain:1

Jan 06, 2025

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: LDLR c.226G>T (p.Gly76Trp) results in a non-conservative amino acid change located in the Low-density lipoprotein receptor domain class A (IPR002172) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251490 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.226G>T has been reported in the literature in individuals affected with Familial Hypercholesterolemia, as well as control cohorts (e.g.Bourbon_2008, Tada_2022, Grzymski_2020, Trinder_2020). These report(s) do not provide unequivocal conclusions about association of the variant with Familial Hypercholesterolemia. At least one publication reports experimental evidence evaluating an impact on protein function (Benito-Vicente_2015). These results showed no damaging effect of this variant on protein expression and localization, or LDL binding and internalization. The following publications have been ascertained in the context of this evaluation (PMID: 25741862, 17765246, 32719484, 36229376, 33079599). ClinVar contains an entry for this variant (Variation ID: 251081). Based on the evidence outlined above, the variant was classified as uncertain significance. -

not provided Uncertain:1

Dec 13, 2023

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Identified in a patient with familial hypercholesterolemia (FH) in published literature (PMID: 17765246); Not observed at significant frequency in large population cohorts (gnomAD); A published functional study suggests the p.(G76W) showed similar levels of expression and trafficking to cell surface compared to wildtype (PMID: 25741862); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.(G55W); This variant is associated with the following publications: (PMID: 32719484, 29261184, 29874871, 27821657, 22881376, 17765246, 25741862) -

Cardiovascular phenotype Uncertain:1

Dec 23, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.G76W variant (also known as c.226G>T), located in coding exon 3 of the LDLR gene, results from a G to T substitution at nucleotide position 226. The glycine at codon 76 is replaced by tryptophan, an amino acid with highly dissimilar properties. This alteration has been reported in a familial hypercholesterolemia (FH) cohort with limited clinical details and in a cohort of 29,906 healthy individuals who underwent multigene panel testing (Bourbon M et al. Atherosclerosis, 2008 Feb;196:633-42; Grzymski JJ et al. Nat Med, 2020 08;26:1235-1239). An in vitro assay showed this alteration may not impact protein function (Benito-Vicente A et al. Genet Med, 2015 Dec;17:980-8). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.48
BayesDel_addAF	Pathogenic	0.54	D
BayesDel_noAF	Pathogenic	0.54
CADD	Pathogenic	31
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.93	D;.;.;.;.
Eigen	Pathogenic	0.89
Eigen_PC	Pathogenic	0.83
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.88	D;D;D;D;D
M_CAP	Pathogenic	0.90	D
MetaRNN	Pathogenic	0.94	D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Uncertain	2.6	M;.;M;M;M
PrimateAI	Benign	0.43	T
PROVEAN	Pathogenic	-6.9	D;D;D;D;D
REVEL	Pathogenic	0.90
Sift	Pathogenic	0.0	D;D;D;D;D
Sift4G	Pathogenic	0.0010	D;D;D;D;D
Polyphen		1.0	D;.;.;.;.
Vest4		0.74
MutPred		0.68		Loss of disorder (P = 0.0198);Loss of disorder (P = 0.0198);Loss of disorder (P = 0.0198);Loss of disorder (P = 0.0198);Loss of disorder (P = 0.0198);
MVP		1.0
MPC		0.88
ClinPred		0.99	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.91
gMVP		0.97

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

LitVar

Other links and lift over

dbSNP: rs574337291; hg19: chr19-11213375;