NM_000518.5:c.20A>T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 10P and 9B. PM5PP5_Very_StrongBP4BA1
The NM_000518.5(HBB):c.20A>T(p.Glu7Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00265 in 1,610,650 control chromosomes in the GnomAD database, including 40 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. E7A) has been classified as Likely benign.
Frequency
Consequence
NM_000518.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.0127 AC: 1926AN: 152176Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00348 AC: 874AN: 251180Hom.: 3 AF XY: 0.00266 AC XY: 361AN XY: 135742
GnomAD4 exome AF: 0.00160 AC: 2335AN: 1458356Hom.: 31 Cov.: 33 AF XY: 0.00145 AC XY: 1054AN XY: 725764
GnomAD4 genome 0.0127 AC: 1937AN: 152294Hom.: 9 Cov.: 32 AF XY: 0.0122 AC XY: 912AN XY: 74478
ClinVar
Submissions by phenotype
Hb SS disease Pathogenic:21Other:1
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Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000015333, PMID:3267215, PS1_S). The variant has been observed in multiple (>3) similarly affected unrelated individuals(PMID: 25023084, 25203083, 25023085, PS4_S). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 1802884, 2296310, 28356267, 12124399, PS3_S). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least one similarly affected unrelated individual (PMID: 23591685, 29542687, PM3_M). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000015126,VCV000036301, PMID:19460936,6129204,8294201, PM5_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (3CNET: 0.83, PP3_P). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
The observed missense variant c.20A>T p.Glu7Val in the HBB gene has been reported previously in multiple individuals with sickle cell disease Meher S et. al., 2016; Akinbami et. al., 2016. Experimental studies have shown that this missense change affects HBB function Eshbach ML et al., 2017. The p.Glu7Val variant has an allele frequency 0.4% in gnomAD Exomes. This variant has been submitted to the ClinVar database as Pathogenic multiple submitters. The amino acid change p.Glu7Val in HBB is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Glu at position 7 is changed to a Val changing protein sequence and it might alter its composition and physico-chemical properties. Computational evidence Polyphen - Benign, SIFT - Damaging and Mutation Taster - Polymorphism predicts conflicting evidence on protein structure and function for this variant. For these reasons, this variant has been classified as Pathogenic. -
While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.53, its frequency in African populations is >5%, as there is a high prevalence of sickle cell disease in African ancestry individuals. -
[ACMG/AMP: PS3, PM3, PM5, PS4_Moderate, PP5] This alteration is supported by well-established in vitro or in vivo functional studies to have a damaging effect on protein function or splicing [PS3], is detected in trans with a known pathogenic variant [PM3], is a novel missense change at an amino residue where a different missense change has been deemed to be pathogenic [PM5], has previously been observed in multiple unrelated patients with the same phenotype [PS4_Moderate], was reported as a pathogenic/likely pathogenic alteration by a reputable source (ClinVar or other correspondence from a clinical testing laboratory) [PP5]. -
The HBB c.20A>T (p.Glu7Val) missense variant, also referred to as p.Glu6Val, has been reported in a homozygous state in more than 1000 individuals with sickle cell anemia (PMID: 25023084; 25023085; 26275168). The highest frequency of this allele in the Genome Aggregation Database is 0.04490 in the African/African-American population (version 2.1.1). This frequency is high, however, carriers are hypothesized to confer protection against Plasmodium falciparum malaria infection (PMID: 21045822). In mice expressing the sickle trait variant, erythrocytes were shown to sickle with deoxygenation, similar to that seen in humans with sickle cell anemia (PMID: 2296310), and in mice with 100% expression of the sickle cell variant, chronic hemolytic anemia with circulating sickled erythrocytes, as well as chronic tissue damage, was observed (PMID: 12124399). Based on the available evidence, the c.20A>T (p.Glu7Val) variant is classified as pathogenic for sickle cell disease. -
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
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The p.Glu7Val variant (also known as p.Glu6Val or hemoglobin S variant) in HBB is a well-established variant which, in the homozygous state, causes sickle cell anemia and which accounts for 60-70% of sickle cell disease in the US (Bender 2003 PMID: 20301551, Serjeant 1968 PMID: 4232783). Co-inheritance with a second HBB variant associated with abnormal hemoglobin (such as Hb C, Hb D, Hb O, Hb E and β-thalassemia pathogenic variants) also results in sickle cell disease. This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 15333) and has been identified in 1799/41432 (4.3%) of African/African American chromosomes, including 9 homozygotes, by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). In vitro functional studies support an impact on protein function as this variant is shown to affect hemoglobin polymerization, resulting in abnormally shaped red blood cells (He 2017 PMID: 12124399, Adachi 1991 PMID: 1802884). Transgenic mouse models have also shown that this variant causes sickle cell disease, as mouse red blood cells with the variant had a sickle shape upon deoxygenation (Greaves 1990 PMID: 2296310). In summary, this variant meets criteria to be classified as pathogenic autosomal recessive sickle cell disease. ACMG/AMP Criteria applied: PM3_Very Strong, PS3. -
PS3, PS4, PM3, PP1 -
A Heterozygous Missense variant c.20A>T in Exon 1 of the HBB gene that results in the amino acid substitution p.Glu7Val was identified. The observed variant has a minor allele frequency of 0.00348% 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, Likely Benign, and Conflicting Interpretations (Variant ID: 15333). This variant has previously been reported for sickle cell anemia by Jaripour ME, et, al., 2018. Experimental studies have shown that this missense change affects HBB function by Eshbach ML, et, al, 2017. Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines. -
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The c.20A>T (p.Glu7Val) variant in HBB (also known as p.Glu6Val) is the most prevalent genotype associated with sickle cell disease (PMID: 25203083). This variant is an established disease-associated mutation and has been reported as pathogenic by multiple clinical diagnostic laboratories in ClinVar (variant ID: 15333). Based on the available evidence, the c.20A>T (p.Glu7Val) variant is classified as pathogenic. -
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The c.20A>T (p.Glu7Val) variant in HBB (also known as p.Glu6Val) is the most prevalent genotype associated with sickle cell disease [PMID: 25203083]. This variant is an established disease-associated mutation and has been reported as pathogenic by multiple clinical diagnostic laboratories in ClinVar (variant ID: 15333). This variant is identified in gnomAD in 1826 heterozygous individuals, 9 homozygous individuals, with an allele frequency of 1.27e-2. Based on the available evidence, the c.20A>T (p.Glu7Val) variant is classified as pathogenic. -
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PS4, PS3, PP1, PP5, PP4. -
not provided Pathogenic:17
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HBB: PM3:Very Strong, PS3:Moderate, PM2:Supporting, PP4, BP4 -
Functional studies using transgenic mouse models showed mouse erythrocytes with this variant sickled upon deoxygenation (Greaves et al., 1990) and kinetic studies indicate this variant drastically decreases the molecular stability of the protein (Adachi et al., 1987); Commonly referred to as p.(E6V) due to the use of alternate nomenclature; This variant is associated with the following publications: (PMID: 20825310, 1802884, 30315176, 3267215, 24123366, 20954261, 22975760, 23065522, 22625666, 19465909, 20305663, 20981092, 22010933, 22028795, 22957039, 23144702, 2296310, 27884173, 27254408, 17393956, 28356267, 26372199, 19758965, 12124399, 22244832, 20861612, 30655275, 30290004, 21329186, 15543018, 30033078, 31553106, 31130284, 31980526, 27650483, 32817264, 32371413, 25023084, 2888754, 31589614, 25087612) -
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This sequence change replaces glutamic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 7 of the HBB protein (p.Glu7Val). This variant is present in population databases (rs334, gnomAD 5%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individuals with sickle cell disease (PMID: 19758965, 20301551, 20861612, 26372199). This variant is also known as p.Glu6Val and HbS. ClinVar contains an entry for this variant (Variation ID: 15333). 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) has been performed at Invitae 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. Experimental studies have shown that this missense change affects HBB function (PMID: 1802884, 12124399, 28356267). For these reasons, this variant has been classified as Pathogenic. -
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The Hb S variant (HBB: c.20A>T; p.Glu7Val, also known as Glu6Val when numbered from the mature protein, HbVar ID: 226, rs334) is a common pathogenic beta globin variant. Heterozygosity for Hb S is consistent with sickle cell trait. Homozygosity for Hb S results in sickle cell anemia. Hb S in combination with a different pathogenic HBB variant on the opposite chromosome results in various forms of sickle cell disease (see HbVar link and references therein). References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html -
beta Thalassemia Pathogenic:5Other:1
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A heterozygous missense variant, NM_000518.5(HBB):c.20A>T, has been identified in exon 1 of 3 of the HBB gene. The variant is predicted to result in a major amino acid change from glutamic acid to valine at position 7 of the protein (NP_000509.1(HBB):p.(Glu7Val)). The glutamic acid at this position has low conservation (100 vertebrates, UCSC), and is located within the Hb-beta like functional domain. In silico predictions of pathogenicity for this variant are conflicting (Polyphen, SIFT, CADD, Mutation Taster). The variant is present in the gnomAD database at a frequency of 0.4% (1228 heterozygous, 4 homozygous). An alternative residue change has been reported in the gnomAD database at a frequency of 0.1%. The variant is the cause of hemoglobin S which results in sickle cell anemia and has been previously described as pathogenic and segregated with disease in multiple families (ClinVar; Kwiatkowski, D.P. 2005). Even though often fatal when homozygous or compound heterozygous, it is seen in high frequency (~10%) in populations in Sub-Saharan African and Middle East where it has been positively selected because it confers protection against malaria in heterozygous individuals, which are asymptomatic (Kwiatkowski, D.P. 2005). Additionally, functional studies showed that erythrocytes from transgenic mice expressing human HBB sickle readily on deoxygenation (Greaves, D.R. et al., 1990). A different variant in the same codon resulting in a change to lysine has been reported to cause a mild hemolytic anemia (ClinVar; Kwiatkowski, D.P. 2005). Based on the information available at the time of curation, this variant has been classified as PATHOGENIC. -
NM_000518.4(HBB):c.20A>T(E7V, aka Hb S) is classified as pathogenic and is associated with hemoglobin S (sickle cell disease). Sources cited for classification include the following: PMID 19061217, 2582106, 22028795, 22625666, 22010933, 2888754, 20954261, 6583683, 1376298. Classification of NM_000518.4(HBB):c.20A>T(E7V, aka Hb S) 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.‚Äã -
Variant classified as Pathogenic and reported on 02-03-2017 by Baylor Medical Genetics Laboratories. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/. -
NM_000518.4:c.20A>T is also known as p.Glu6Lys or HbS in the literature. NM_000518.4:c.20A>T in the HBB gene has an allele frequency of 0.045 in African subpopulation in the gnomAD database. The c.20A>T (p.Glu7Val) variant in HBB is the most prevalent genotype associated with sickle cell disease (PMID: 25203083). Kondani et al reported that among 247 children, 19 (7.7%) were homozygous sickle cell anemia patients (Hb SS) (PMID: 25023084). Experimental studies have shown that this missense change affects hemoglobin polymerization and can result in abnormally-shaped red blood cells (PMID: 12124399; 28356267; 1802884). Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PS4; PS3; PM3; PP4. -
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Beta-thalassemia HBB/LCRB Pathogenic:4
The variant HBB:c.20A>T [NP_000509.1:p.Glu7Val ] , produce sickle hemoglobin (HbS), it is a beta+ mutation. Homozygous of this variant is responsible for sickle cell anaemia . In combination with other beta mutation it may cause wide variety of sickle beta phenotype. The frequency of this allele in different state of India varies from 2 % to 20% (Ref: PMID: 30523337] . The frequency of this variant among hemoglobinopathy patient in West Bengal is less than 3.8 % as per 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]. -
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The missense c.20A>T (p.Glu7Val) variant in HBB gene has been reported previously in homozygous and compound heterozygous state in multiple individuals affected with HBB-related sickle cell anemia (Akinbami et al. 2016; Meher et al. 2016). Experimental studies have shown that this mutation (Glu7Val) in hemoglobin (Hb) causes red blood cells to assume a rigid curved shape that blocks their passage through the vasculature resulting in ischemia, severe pain, and necrosis (Eshbach et al. 2017). The p.Glu7Val variant has 0.4% allele frequency in gnomAD exomes database. This variant has been reported to the ClinVar database as Pathogenic (multiple submissions). The amino acid change p.Glu7Val in HBB is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Glutamic acid at position 7 is changed to a Valine 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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HBB-related disorder Pathogenic:3Other:1
Variant identified in multiple registry participants. Variant interpreted as consistent with alpha thalassemia trait and reported on 02-28-2020 by Lab or GTR ID 500068. Variant interpreted as Pathogenic and reported on 07-21-2020 by Lab or GTR ID 1197. Variant interpreted as Pathogenic and reported on 05-26-2021 by Lab or GTR ID 20290. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
The HBB c.20A>T variant is predicted to result in the amino acid substitution p.Glu7Val. This variant, also referred to as p.Glu6Val using legacy nomenclature, has previously been reported to be causative for sickle cell anemia when present in the homozygous state (Engelke et al. 1988. PubMed ID: 3267215; Bender et al. 2017. PubMed ID: 20301551). Individuals heterozygous for this variant have sickle cell trait and are usually asymptomatic but can be at risk for complications, including exertional rhabdomyolysis, pulmonary emboli, and sudden death with extreme exertion (Key and Derebail. 2010. PubMed ID: 21239829; Bender et al. 2023. PubMed ID: 20301551). This variant is reported in 4.5% of alleles in individuals of African descent in gnomAD. We interpret this variant as pathogenic. -
The c.20A>T (p.Glu7Val) variant in HBB, also known as p.Glu6Val, is referred to as the hemoglobin S allele (HbS) and causes autosomal recessive sickle cell disease (MIM: #603903) when it is homozygous or compound heterozygous with a different pathogenic variant. Individuals who are heterozygous for the HbS allele have sickle cell trait (SCT). The c.20A>T (p.Glu7Val) variant is the most prevalent genotype associated with sickle cell disease (PMID: 25203083). This variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. It is present at a frequency of 0.4% (1236/282580 heterozygotes and 4/282580 homozygotes) in the gnomAD population database. The c.20A>T (p.Glu7Val) variant is an established disease-causing mutation. Based on the available evidence, c.20A>T(p.Glu7Val) is classified as Pathogenic. -
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 13464827; 11880644; 11830454; 12124399; 28356267; 1802884) - PS3.The c.20A>T;p.(Glu7Val) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 15333; PMID: 20301551; PMID: 30002798; PMID: 15658184;PMID: 7384810; PMID: 6268660; PMID: 26372199; PMID: 26275168; PMID: 28356267; PMID: 22625666; PMID: 32527859) - PS4. The p.(Glu7Val) was detected in trans with a pathogenic variant (PMID: 15658184; PMID: 20861612; PMID: 21131035) - PM3_very strong. Pathogenic missense variant in this residue have been reported (ClinVar ID: 15126 PMID: 20301551; 27117572; 26372199) - PM5. The variant co-segregated with disease in multiple affected family members (PMID: 21302591; 34334128; 14084634; 26041415) - PP1_strong.and allele frequency is greater than expected for disorder - BS1. In summary, the currently available evidence indicates that the variant is pathogenic. -
Inborn genetic diseases Pathogenic:1
The c.20A>T (p.E7V) alteration is located in exon 1 of the HBB gene. This alteration results from a A to T substitution at nucleotide position 20, causing the glutamic acid (E) at amino acid position 7 to be replaced by a valine (V). Based on data from gnomAD, the T allele has an overall frequency of 0.44% (1236/282580) total alleles studied. The highest observed frequency was 4.49% (1121/24964) of African/African American alleles. This alteration results in the hemoglobin S (HbS) variant and is associated with sickle cell disease (Ingram, 1956). This amino acid position is not well conserved in available vertebrate species. The p.E7V alteration is known to significantly decrease the solubility of the hemoglobin protein, allowing for the polymerization that ultimately results in red cell sickling (Adachi, 1987). The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic. -
Sickle cell-hemoglobin C disease Pathogenic:1
This HBB variant (rs334) reaches polymorphic frequency (>1%) within the African/African American subpopulation in a large population dataset (gnomAD: 1121/24964 total alleles; 4.49%; 4 homozygotes) and has been reported in ClinVar. It is the most common pathogenic HBB variant in individuals of African ancestry. Also known as p.Glu6Val and HbS, it has been reported in a homozygous or compound heterozygous state in individuals with beta-hemoglobinopathies. One bioinformatic tool queried predicts that this substitution would damaging, while another predicts it would be tolerated. Experimental studies have shown that this variant affects the physical and kinetic properties of the hemoglobin protein. Bioinformatic analysis predicts that this missense variant would not affect normal exon 1 splicing, although this has not been confirmed experimentally to our knowledge. We consider c.20A>T (p.Glu7Val) to be 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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Hb SS disease;C0005283:beta Thalassemia;C0700299:Heinz body anemia;C1841621:Fetal hemoglobin quantitative trait locus 1;C1858990:Dominant beta-thalassemia;C1970028:Malaria, susceptibility to Pathogenic:1
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Fetal hemoglobin quantitative trait locus 1 Pathogenic:1
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See cases Pathogenic:1
ACMG classification criteria: PS3, PS4, PM3, BS1 -
Sickle cell disease and related diseases Pathogenic:1
Variant summary: HBB c.20A>T (p.Glu7Val) results in a non-conservative amino acid change located in the Globin domain (IPR000971) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0035 in 251180 control chromosomes in the gnomAD database, including 3 homozygotes. c.20A>T has been reported in the literature in multiple individuals affected with Sickle Cell Disease, an inherited monogenic disease characterized by intravascular sickling, haemolysis, anemia and leukocytosis as well as the association between sickled red blood cells and other blood components (example, Domingos_2014). 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. The most pronounced variant effect results in decreased solubility of deoxygenated Hb S, and polymerization which leads to the formation of an extensive network of fibers in red blood cells (example, Adachi_1991). Eleven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
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:1
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Malaria, resistance to Benign:1
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HEMOGLOBIN S Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at