chr11-5226943-C-T
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM5PP3PP5_Very_Strong
The NM_000518.5(HBB):c.79G>A(p.Glu27Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000224 in 1,613,724 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E27V) has been classified as Likely benign.
Frequency
Consequence
NM_000518.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.000420 AC: 64AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000255 AC: 64AN: 251352Hom.: 1 AF XY: 0.000317 AC XY: 43AN XY: 135844
GnomAD4 exome AF: 0.000204 AC: 298AN: 1461396Hom.: 5 Cov.: 33 AF XY: 0.000275 AC XY: 200AN XY: 727050
GnomAD4 genome 0.000414 AC: 63AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.000631 AC XY: 47AN XY: 74486
ClinVar
Submissions by phenotype
not provided Pathogenic:7
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Published functional RNA studies demonstrate that this variant is associated with slow excision of intron 1 and alternative splicing into exon 1 (Orkin et al., 1982); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 25370867, 12144064, 15481886, 22975760, 18024613, 6166632, 24123366, 6198908, 3728469, 29669226, 22028795, 22260787, 7177196, 26554862, 12149194, 24368026, 17278112, 27834070, 9140717, 7583766, 31553106, 1878422, 31980526, 30275481, 31589614, 10870880, 31890591, 8629114, 28674233, 34794358, 33092414, 29251006, 28671035, 35047849, 21732929) -
This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 27 of the HBB protein (p.Glu27Lys). This variant is present in population databases (rs33950507, gnomAD 0.1%). This missense change has been observed in individual(s) with beta thalassemia (PMID: 21732929, 26554862). It has also been observed to segregate with disease in related individuals. This variant is also known as Hb E and Glu26Lys. ClinVar contains an entry for this variant (Variation ID: 15161). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on HBB protein function. Studies have shown that this missense change alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 21732929, 22260787). For these reasons, this variant has been classified as Pathogenic. -
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The Hb E variant (HBB: c.79G>A; p.Glu27Lys, also known as Glu26Lys when numbered from the mature protein, rs33950507, HbVar ID: 277) is a common pathogenic beta globin variant. Functional characterization of the variant indicates aberrant splicing of the beta globin mRNA, leading to reduced mature protein (Orkin 1982). Heterozygous Hb E is a clinically benign condition associated with mild microcytosis and target cells without anemia. Homozygous Hb E is usually a clinically benign condition but can be associated with mild anemia and microcytosis. Hb E in combination with a different pathogenic HBB variant on the opposite chromosome can produce a range of clinical phenotypes (Vichinsky 2007, HbVar database and references therein). REFERENCES Link to HbVar database: https://globin.bx.psu.edu/hbvar/hbvar.html Orkin S et al. Abnormal RNA processing due to the exon mutation of beta E-globin gene. Nature. 1982; 300(5894):768-9. PMID: 7177196. Vichinsky E Hemoglobin e syndromes. Hematology Am Soc Hematol Educ Program. 2007:79-83. PMID: 18024613. -
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beta Thalassemia Pathogenic:6
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NM_000518.4(HBB):c.79G>A(E27K, aka Hb E) is classified as pathogenic and is associated with hemoglobin E disease. Sources cited for classification include the following: PMID: 17278112, 7177196, 7395858, 22028795, 6166632, and 24368026. Classification of NM_000518.4(HBB):c.79G>A(E27K, aka Hb E) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. -
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The p.Glu27Lys variant in HBB, also known as p.Glu26Lys and the cause of hemoglobine E disease, has been reported in numerous individuals in the heterozygous (asymptomatic), homozygous (asymptomatic to mild to moderate hemolytic microcytic anemia with or without hepatosplenomegaly and jaundice) and in the compound heterozygous state with another pathogenic variant for beta-thalassemia (phenotypes ranging from mild to moderate beta-thalassemia (Orkin 1982 PMID: 7177196, Tubsuwan 2011 PMID: 21732929, Prajantasen 2014 PMID: 25370867, Jayasree 2016 PMID: 26554862). It has been reported in ClinVar (Variation ID 15161) and it has been identified in 41/4836 South Asian chromosomes by gnomAD (https://gnomad.broadinstitute.org/). In vitro functional studies showed that this variant produces both a structurally abnormal Hb and creates a cryptic 5' splice site that causes abnormal mRNA splicing; in addition transgenic mice exclusively expressing human p.Glu27Lys had red blood cell mild oxidative stress arising in part from the molecular consequences of the p.Glu27Lys variant (Chen 2012 PMID: 22260787). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive beta thalassemia. ACMG/AMP Criteria applied: PM3_very Strong, PS3_Strong. -
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
Beta-thalassemia HBB/LCRB Pathogenic:6
A Heterozygous Missense variant c.79G>A in Exon 1 of the HBB gene that results in the amino acid substitution p.Glu27Lys was identified. The observed variant has a minor allele frequency of 0.00025/0.00006% in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is medium, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic (Variant ID: 15161). This variant has been identified in patients affected with beta-thalassemia (Tubsuwan A et al., 2011). Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines. -
The HBB variant c.79G>A (beta+), which results in unstable Hemoglobin E, is clinically benign when present in compound heterozygous with other Beta zero mutation. Accrpdingly when this variant occurs alongside other pathogenic HBB variants, it can lead to varying degrees of anemia. The frequency of this variant varies across different populations in India.The prevalence of this variant shows significant regional differences. In the Bengali population of Eastern India, the prevalence is notably high at approximately 33.23%, whereas in the Northern Indian population, the frequency is very low, at around 0.2% among thalassemia patients. According to our multicentric Multicentric Project - A Genetic Diagnostic Algorithm Based Study for Thalassemia in Northern and Eastern Indian Populations", Funded by Dept. of Biotechnology , Govt of India [Project No. BT/PR26461/MED/12/821/2018], -
The missense c.79G>A(p.Glu27Lys) variant in HBB gene has been reported in both homozygous and heterozygous states in multiple individuals affected with hemoglobin-related disorder (Prajantasen et al., 2014; Jayasree et al., 2016). Studies have shown that this missense change alters mRNA splicing and is expected to lead to the loss of protein expression (Chen Q et. al., 2012). This variant is reported with allele frequency of 0.02% in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant has been submitted to the ClinVar database as Pathogenic (multiple submissions). The amino acid change p.Glu27Lys in HBB is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. Multiple lines of computational evidence (Polyphen, SIFT and MutationTaster) predict a conflicting evidences on protein structure and function for this variant. The amino acid Glu at position 27 is changed to a Lys changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic. -
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Variant summary: HBB c.79G>A (p.Glu27Lys), also known as Hb E, results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. Several computational tools predict a significant impact on normal splicing: three predict the variant strengthens a cryptic 5' donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing, finding that only 5-8% of mRNA is correctly spliced due to the creation of a cryptic splice donor site, leading to the loss of the last 16 bases of the exon (e.g., Chen_2012). The variant allele was found at a frequency of 0.00025 in 251352 control chromosomes in the gnomAD database, including 1 homozygotes, but c.79G>A is a known, common disease variant. This variant has been reported in the homozygous state in numerous patients in the literature (e.g., Pakdee_2014, Sanchaisuriya_2006). Hb E homozygosity results in a mild beta-globin chain deficit which is comparable to that seen in beta0-thal heterozygotes, and homozygotes typically have mild hemolytic anemia and mild enlargement of the spleen. However, compound heterozygotes for hemoglobin E/-thalassemia are often severely affected. Conditions in which there is a considerable production of Hb A are milder than those without Hb A. These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function, finding that the variant results in increased reactive oxygen species as well as mild oxidative stress (e.g., Chen_2012). The following publications have been ascertained in the context of this evaluation (PMID: 22260787, 24581976, 16750922). ClinVar contains an entry for this variant (Variation ID: 15161). Based on the evidence outlined above, the variant was classified as pathogenic. -
Hemoglobin E disease Pathogenic:2
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. 0102 - Loss of function is a known mechanism of disease in this gene and is associated with HBB-related hemoglobinopathies, including beta thalassemia (OMIM). Dominant negative is also a suggested mechanism (PMID: 29700171). (I) 0108 - This gene is associated with both recessive and dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity. Variable severity has been reported in sickle cell patients carrying the same variants (PMID: 31788855). In addition, clinical severity of beta-thalassemia patients is also dependent on whether variants in HBB are heterozygous, homozygous or compound heterozygous, and the amount of residual protein that is expressed (GeneReviews). (I) 0200 - Variant is predicted to result in a missense amino acid change from glutamic acid to lysine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 (v2: 64 heterozygotes, 1 homozygote). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated globin domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. Also known as p.(Glu26Lys) and the HbE variant, it has been identified in at least ten patients and is known as a pathogenic structural variant. (GeneReviews; ClinVar, PMID: 28546763). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
The HBB c.79G>A (p.Glu27Lys) variant, also referred to as p.Glu26Lys, is well-described and the singular cause of hemoglobin E disorder (HbE). Though common throughout the world, the p.Glu27Lys variant is found at the greatest frequency in Southeast Asia (Chen et al. 2012). Individuals who are heterozygous for the p.Glu27Lys variant are asymptomatic, while the clinical phenotypes of at least 85 individuals who are homozygous for the variant ranged from asymptomatic to mild to moderate hemolytic microcytic anemia with or without hepatosplenomegaly and jaundice (Prajantasen et al. 2014; Jayasree et al. 2016). Individuals compound heterozygous for p.Glu27Lys and a pathogenic variant for beta-thalassemia can have disease phenotypes ranging from beta-thalassemia intermedia to beta-thalassemia major (Origa et al. 2015). The p.Glu27Lys variant was identified in a compound heterozygous state with a pathogenic beta thalassmia variant in at least 38 individuals who were reported to have mild to moderate thalassemia, 29 of whom required treatment with blood transfusions (Tubsuwan et al. 2011). The variant is reported at a frequency of 0.015152 in the Kinh in Ho Chi Minh City, Vietnam, population of the 1000 Genomes Project. Functionally, the p.Glu27Lys variant is known to produce both a structurally abnormal Hb and a cryptic 5' splice site that causes abnormal mRNA splicing, and transgenic mice exclusively expressing human p.Glu27Lys had red blood cell mild oxidative stress arising in part from the molecular consequences of the p.Glu27Lys variant (Chen et al. 2012). Based on the collective evidence, the p.Glu27Lys variant is classified as pathogenic for hemoglobin E. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Hb SS disease;C0019025:Hereditary persistence of fetal hemoglobin;C0700299:Heinz body anemia;C1840779:METHEMOGLOBINEMIA, BETA TYPE;C1858990:Dominant beta-thalassemia;C1970028:Malaria, susceptibility to;C4693822:Erythrocytosis, familial, 6;CN322236:Beta-thalassemia HBB/LCRB Pathogenic:2
PS3_Moderate+PM3_VeryStrong+PP4 -
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Hb SS disease Pathogenic:1Other:1
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Hemoglobin E/beta- thalassemia Pathogenic:1
Previously known variant, c.79G>A p.(Glu27Lys) (Saha J et. al., 2021; Accession: VCV000015161.140) in exon 1 of HBB is observed in compound heterozygous state in Proband. Segregation analysis in the family showed that the variant, c.79G>A was present in heterozygous state in her mother. Hemoglobin electrophoresis and the clinical findings observed in the proband are in concordance with hemoglobin E/beta-thalassemia. -
Hemoglobin E/beta thalassemia disease Pathogenic:1
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Inborn genetic diseases Pathogenic:1
The p.E27K pathogenic mutation (also known as c.79G>A, Hb E, and E26K), located in coding exon 1 of the HBB gene, results from a G to A substitution at nucleotide position 79. The glutamic acid at codon 27 is replaced by lysine, an amino acid with similar properties. Hb E is a common hemoglobin variant prevalent among Southeast Asian individuals. The combination of Hb E and beta-thalassemia is frequently associated with a moderately severe phenotype, due to a primary reduction of beta-E-globin synthesis resulting from decreased accumulation of beta-E-globin mRNA (Benz EJ et al. J. Clin. Invest., 1981 Jul;68:118-26). Abnormal RNA processing occurs due to activation of a cryptic splice donor site in exon 1 (Orkin SH et al. Nature, 1982 Dec;300:768-9). Overall, compound heterozygosity for Hb E beta-thalassemia may result in a variable phenotype ranging from asymptomatic to transfusion dependency, though Hb E beta-zero-thalassemia is typically severe and may be similar to thalassemia major or intermedia (Vichinsky E. Hematology Am Soc Hematol Educ Program, 2007;:79-83). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Anemia Pathogenic:1
The c.79G>A variant is observed in 35/30782 (0.11%) alleles from individuals of South Asian background in the gnomAD population database. In silico splice prediction models predict that c.79G>A may enhance a cryptic splice donor site upstream of the natural splice donor site in intron 1, which may supplant the natural donor site. RNA studies demonstrate that this variant is associated with slow excision of intron 1 and alternative splicing into exon 1 (PMID 7177196). If c.79G>A does not alter splicing, it will result in the E27K missense change, also commonly referred to as E26K due to the use of alternative nomenclature. The E27K variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Based on the available evidence, the c.79G>A, p.Glu27Lys is classified as Pathogenic. -
HBB-related disorder Pathogenic:1
The HBB c.79G>A variant is predicted to result in the amino acid substitution p.Glu27Lys. This variant, commonly referred to as Hemoglobin E/HbE, has previously been reported to cause hemoglobinopathy (HbVar; http://globin.bx.psu.edu/hbvar; Vichinsky. 2007. PubMed ID: 18024613). Historically, this variant was reported as p.Glu26Lys (Orkin et al. 1982. PubMed ID: 7177196). In the ClinVar database, this variant has also been interpreted as pathogenic by several different laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/15161/). Homozygous HbE has been reported in many patients and can be associated with mild hemolytic anemia (Masiello et al. 2007. PubMed ID: 17278112; Jayasree et al. 2016. PubMed ID: 26554862; Origa et al. 2018. PubMed ID: 20301599). This variant is classified as pathogenic. -
alpha Thalassemia;C0002895:Hb SS disease;C0005283:beta Thalassemia;C0700299:Heinz body anemia;C1840779:METHEMOGLOBINEMIA, BETA TYPE;C1841621:Fetal hemoglobin quantitative trait locus 1;C1858990:Dominant beta-thalassemia;C1970028:Malaria, susceptibility to;C4693822:Erythrocytosis, familial, 6 Pathogenic:1
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Malaria, susceptibility to Pathogenic:1
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Hereditary persistence of fetal hemoglobin Pathogenic:1
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Beta-plus-thalassemia Pathogenic:1
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not specified Pathogenic:1
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Malaria, resistance to Benign:1
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Hemoglobin E Other:1
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Hb SS disease;C0019025:Hereditary persistence of fetal hemoglobin;C0700299:Heinz body anemia;C1840779:METHEMOGLOBINEMIA, BETA TYPE;C1858990:Dominant beta-thalassemia;C4693822:Erythrocytosis, familial, 6;CN322236:Beta-thalassemia HBB/LCRB Other:1
Variant classified as not provided and reported on 06-23-2021 by Unknown Russian Laboratory. GenomeConnect-CFC International assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at