ClinVar Genomic variation as it relates to human health

Variant summary: LDLR c.631C>T (p.His211Tyr) results in a conservative amino acid change located in the Low-density lipoprotein (LDL) receptor class A repeat of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 246024 control chromosomes (gnomAD). The variant, c.631C>T, has been reported in the literature in individuals affected with Familial Hypercholesterolemia (Ahmad_2012), but was also found to not segregate with disease in one family study (Hopkins_1999). Since the penetrance of Familial Hypercholesterolemia (0.75) due to this variant appears to be lower than expected (0.8) and no individual in the family study had a history of coronary artery disease or tendon xanthomas, no conclusions can be drawn from these data. Two different missense substitutions at the same codon as the variant of interest (c.631C>G (His 211Asp) and c.632A>T (H190L)) have been reported in individuals affected with familial hypercholesterolemia (Sanchez-Hernandez_2016, Widhalm_2007), suggesting this codon might be functionally important. In vitro studies have shown that mutation of any individual LDLR histidine to tyrosine (H190Y, H562Y, or H586Y; legacy names) does not interfere with the ability of the receptor to bind LDL at neutral pH on the cell surface, nor is the LDL-release activity diminished by more than about 30% when compared with normal LDLR activity, with one of the authors suggesting that this variant might be a receptor polymorphism (Huang_2010, Beglova_2004). However, it has been shown that when all three histidines are simultaneously replaced by either alanine or tyrosine, the mutant receptor loses the ability to release bound LDL (Huang_2010). These studies suggest that in isolation, this variant has little functional impact on LDL binding or release. One ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cites the variant as pathogenic, while two literature reviews cite it as likely pathogenic/pathogenic. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic, until more definitive functional and clinical data become available.

Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt LDLR protein function. This sequence change replaces histidine, which is basic and polar, with tyrosine, which is neutral and polar, at codon 211 of the LDLR protein (p.His211Tyr). This variant is present in population databases (rs771917370, gnomAD 0.006%). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 1057090, 23064986). It has also been observed to segregate with disease in related individuals. This variant is also known as p.His190Tyr. ClinVar contains an entry for this variant (Variation ID: 251335). Experimental studies have shown that this missense change affects LDLR function (PMID: 21511053). This variant disrupts the p.His221 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17347910, 27784735). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

This missense variant replaces histidine with tyrosine at codon 211 of the LDLR protein. This variant is also known as p.His190Tyr in the mature protein. This variant alters a conserved histidine residue in the ligand binding domain LDLR type A repeat 4 of the LDLR protein LDLR type A repeat 4 (a.a. 146-186), where pathogenic missense variants are found enriched (ClinVar-LDLR). Computational prediction suggests that this variant may have a deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Multiple functional studies have shown that this variant has a mild impact on LDLR protein expression and function (PMID: 15494314, 15741231, 19674976, 21511053). This variant has been reported in four siblings affected with familial hypercholesterolemia (PMID: 10570905) and in three unrelated individuals affected with familial hypercholesterolemia (UMD, PMID: 23064986; communication with external laboratories: ClinVar SCV002660614.1, UMD). It has also been reported in 6 individuals suspected to be affected with familial hypercholesterolemia (PMID: 34037665). This variant has been identified in 3/250972 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic.

This missense variant replaces histidine with tyrosine at codon 211 of the LDLR protein. This variant is also known as p.His190Tyr in the mature protein. This variant alters a conserved histidine residue in the ligand binding domain LDLR type A repeat 4 of the LDLR protein LDLR type A repeat 4 (a.a. 146-186), where pathogenic missense variants are found enriched (ClinVar-LDLR). Computational prediction suggests that this variant may have a deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Multiple functional studies have shown that this variant has a mild impact on LDLR protein expression and function (PMID: 15494314, 15741231, 19674976, 21511053). This variant has been reported in four siblings affected with familial hypercholesterolemia (PMID: 10570905) and in three unrelated individuals affected with familial hypercholesterolemia (UMD, PMID: 23064986; communication with external laboratories: ClinVar SCV002660614.1, UMD). It has also been reported in 6 individuals suspected to be affected with familial hypercholesterolemia (PMID: 34037665). This variant has been identified in 3/250972 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic.

The p.His211Tyr variant in LDLR (also described as p.His190Tyr in the literature) has been reported in the heterozygous state in 2 individuals with familial hypercholesterolemia (FH) and segregated with disease in 4 affected relatives from 1 family (Hopkins 1999, Ahmad 2012). It has also been reported by other clinical laboratories in ClinVar (Variation ID 251335) and has been identified in 3/250972 of pan-ethnic chromosomes by gnomAD (http://gnomad.broadinstitute.org). This frequency is low enough to be consistent with the frequency of FH in the general population. An in vitro functional study and computational prediction tools support an impact to the protein. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant FH. ACMG/AMP criteria applied: PM2, PP1, PP3, PS3_Supporting, PS4_Supporting.

The p.H211Y pathogenic mutation (also known as c.631C>T), located in coding exon 4 of the LDLR gene, results from a C to T substitution at nucleotide position 631. The histidine at codon 211 is replaced by tyrosine, an amino acid with similar properties, and is located in the ligand binding domain. This alteration, historically described as p.H190Y, has been detected in individuals with familial hypercholesterolemia (FH), with segregation reported in at least four affected relatives from one family (Hopkins PN et al. J. Hum. Genet., 1999;44:364-7; Ahmad Z et al. Circ Cardiovasc Genet, 2012 Dec;5:666-75). Internal structural analysis has determined this variant to be located in an LDLR hotspot region, and alternate amino acid substitutions at this position, p.H211L (p.H190L) and p.H211D (p.H190D), have been reported in FH cohorts (Rudenko G et al. Science, 2002 Dec;298:2353-8; Widhalm K et al. J. Inherit. Metab. Dis., 2007 Apr;30:239-47; Bourbon M et al. Atherosclerosis, 2008 Feb;196:633-42). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

The c.631C>T (p.His211Tyr) variant in the LDLR gene is located on the exon 4 and is predicted to replace histidine with tyrosine at codon 211 (p.His211Tyr). The variant has been identified in an individual with familial hypercholesterolemia (FH) (PMID: 23064986). It segregated with FH phenotype in 4 informative meiosis in a family (LDL-c higher than 190 mg/dL) (PMID: 10570905). Functional study of this variant with LDLR deficient fibroblast cells showed the LDL uptake was close to 70% of WT and had marginal impact (PMID: 21511053). The variant has been reported in ClinVar (ID: 251335). The variant is rare in the general population according to gnomAD (3/250972, PopMax MAF<0.02%). Computational prediction algorithms suggest a deleterious impact for this variant (REVEL score 0.896). Therefore, the c.631C>T (p.His211Tyr) variant of LDLR has been classified as likely pathogenic.

Functional studies demonstrate this variant decreases the lipoprotein-binding capacity of the LDL receptor through reduction in the number of surface receptors; however, the effect on surface expression did not reach statistical significance (PMID: 21511053); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as H190Y; This variant is associated with the following publications: (PMID: 15494314, 15741231, 18847225, 29204877, 26755827, 10570905, 32719484, 34037665, 23064986, 34906454, 21511053, 38852422, 30583242)

Variant p.His211Tyr in LDLR c.631C>T in exon 4 (NM_000527.4, hg19, chr19-11216213-C-T) This variant is also known as p.His190Tyr in the literature. SCICD classification Pathogenic We do feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). The rationale for this assessment is: moderate case and segregation data, strong functional studies and rarity in the general population. Gene-level evidence LDLR: LDL receptors are located on the surface of the liver and play an important role in LDL recycling. Pathogenic variants in LDLR account for 80% of cases of familial hypercholesterolemia. Both missense and truncating/frameshift variants can be pathogenic. Case data summary Cases (not including our patient): At least 3 individuals with FH or homozygous FH. Segregated with disease in 4 additional family members from one of these families. Found in two family members who did not have elevated cholesterol, one of whom was 3 years old at the time of testing. ClinVar: classified as likely pathogenic by one lab and pathogenic by onelabs. The Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde,Academisch Medisch Centrum has also seen this variant but do not provide a classification. Please see below for a detailed review of case data. Predicted Consequence Per the test report, "This sequence change replaces histidine with tyrosine at codon 211 of the LDLR protein (p.His211Tyr)." Histidine is a positively charged amino acid whereas tyrosine is an amino acid with a hydrophobic side chain. Experimental Data Detailed functional studies have shown that this missense change impairs LDLR protein function in vitro. This is true for this variant as well as for others at this codon. This variant is located in a region of the LDL receptor (LA4) that is important for binding LDL molecules. Conservation Per the test report, "The histidine residue is highly conserved and there is a moderate physicochemical difference between histidine and tyrosine." The amino acid histidine is strongly, though not completely conserved in aligned species in the UCSC genome browser. Nearby pathogenic variation Per Varsome.org, there is another variant present in ClinVar at this codon, with conflicting interpretations. There are several other nearby pathogenic or likely pathogenic variants listed in ClinVar per Varsome.org Population Data Highest MAF in Latino population: 0.0059%. Metrics indicate adequate coverage. Please see below for details. Case data for p.His211Tyr in LDLR (does not include this patient): At least 6 individuals with familial hypercholesterolemia have this variant. This variant was reported to segregate in 4 individuals in one family with FH. The variant was present in two individuals who did not have high cholesterol, though one was only 3 years old. The authors attributed this to age-dependent penetrance. We consider this moderate segregation data. ClinVar: Pathogenic: Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge Likely pathogenic: LDLR-LOVD, British Heart Foundation No interpretation: Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde,Academisch Medisch Centrum Cases in the literature: At least 3 individuals with FH or homozygous FH. This variant segregated with disease in 4 family members tested. An additional family member did not have the phenotype but had the variant. A young child did not have elevated cholesterol but was only 3 years of age. Hopkins et al 1999: Variant referred to as p.His190Tyr in this paper. Caucasian proband from Utah with LDL cholesterol levels of 277 mg/dL and their affected relatives with high cholesterol (see pedigree below) underwent sequencing of the LDLR gene which revealed p.His190Tyr. This variant segregated in all family members with elevated cholesterol (shaded in black in the diagram below). It is important to note ages here. The reduced penetrance of this variant in individual III-3 was puzzling to the authors. IV-1 may not have developed elevated cholesterol at this time. Therefore, I would conclude that this study provided 4 additional segregations for this variant and did not segregate with disease in another. The authors suggest that III-3 may have other protective genetic factors that keep LDL cholesterol within the normal range. Bourbon et al 2008: H190D found in 1 out of 184 Portuguese patients with FH. This patient was 1 of 4 patients with homozygous FH. H190Y was present in compound heterozygous form with an additional frameshift variant and an additional missense variant. The parents were not available for genetic testing, so it was not possible to determine phase. The patient was a 29-year-old male at the time of publication whose LDL-c level prior to treatment was 515 mg/dL, which was reduced to 298 mg/dL on treatment. His past medical history included a myocardial infarction at 23 years old followed by a CABG and angioplasty at 24 years old. Ahmad et al 2012: 1 individual of Hispanic descent of 91 patients with autosomal dominant hypercholesterolemia. LDL-C ranged from 175 to 397 mg/dL in this population, although we do not know the cholesterol levels for this particular patient. Functional studies Beglova et al 2004: p.His190Tyr bound LDL at a neutral pH and released the ligand in response to a low pH but with lower efficiency than wild type. The authors repeated it with alanine. Per this study, histidine at position 190 directly participate in the release of LDL. Huang et al 2010: H190Y had effects on acid-dependent LDL release in vitro assays and bound less LDL than wild type. Zhao et al 2011: This variant is known as H190Y in this paper. This variant is present in the LA5 domain. The LA4 and LA5 domain are integral for all lipoprotein binding. The authors suggest that H190, in its native state, may make ionic contact with a residue in LA4 and this interaction is integral for lipoprotein binding. The pKa of histidine is similar to the pH necessary to drive LDL release. Replacing a histidine with a tyrosine reduces acid sensitivity of LDL release. Expressed H190Y in full-length LDL receptors in deficient fibroblasts and compared the ability of these cells versus wild type to uptake LDL and beta-VLDL. H190Y impaired lipoprotein uptake. The authors concluded that reduced surface expression was likely responsible for the reduced LDL uptake. Per this data, H190Y is a loss-of-function variant that may reduce the fraction of receptors that transits through the ER-Golgi system and is classified as a Class 2 FH mutation. Per the authors, Class 2 FH mutations are the most common type of FH mutation observed in LA5. Many other variants near H190Y have been observed to hinder refolding of LA5. Azevedo 2015 thesis: Variant found in 2 out of 25 unrelated Portuguese individuals with FH and 3 of their family members. Confirmed that this variant presents normal expression on the cell surface but only 50% binding activity is observed and uptake of LDL is reduced by 50%. Data for other variants at this codon: Sánchez-Hernández et al 2016: Other variants at this codon (His211Asp): noted in 4 out of 97 Spanish patients with homozygous FH in the presence of another pathogenic variant (compound heterozygous rather than homozygous). Yamamoto et al 2008: The effect of variants at position 190 was studied at pH 7. Ligand binding to the His190Lys receptor was poor compared to the native amino acid. Population data for p.His211Tyr in LDLR: Highest MAF in Latino population: 0.005956%. The variant was reported online in 3 of 123,012 total individuals (MAF: 0.005956%) in the Genome Aggregation Consortium Dataset (gnomAD; http://gnomad.broadinstitute.org/), which currently includes variant calls on >140,000 unrelated individuals of African, Asian, European, Ashkenazi, and Latino descent. Specifically, the variant was observed in: 2 of 16,791 individuals of Latino descent (MAF=0.005956%) 1 of 15,391 individuals of South Asian descent (MAF=0.003249%) The phenotype of those individuals is not publicly available. The dataset is composed of multiple cohorts, some of which were recruited from the general population, others were enriched for common cardiovascular disease. As of January 17, 2018 the average coverage at that site in gnomAD for exomes is: Mean coverage 86.8x, Median coverage 100x, and 99.33% of samples over 20x coverage. No variant detected in genomes.