ClinVar Genomic variation as it relates to human health
NM_000517.6(HBA2):c.377T>C (p.Leu126Pro)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000517.6(HBA2):c.377T>C (p.Leu126Pro)
Variation ID: 15630 Accession: VCV000015630.19
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 16p13.3 16: 173548 (GRCh38) [ NCBI UCSC ] 16: 223547 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Sep 29, 2024 Feb 16, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000517.6:c.377T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000508.1:p.Leu126Pro missense NC_000016.10:g.173548T>C NC_000016.9:g.223547T>C NG_000006.1:g.34411T>C NG_046165.1:g.3287T>C NG_059186.1:g.1898T>C NG_059271.1:g.5702T>C LRG_1225:g.1898T>C LRG_1240:g.5702T>C LRG_1240t1:c.377T>C LRG_1240p1:p.Leu126Pro P69905:p.Leu126Pro - Protein change
- L126P
- Other names
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L125P
Alpha2 Leu125Pro
- Canonical SPDI
- NC_000016.10:173547:T:C
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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Trans-Omics for Precision Medicine (TOPMed) 0.00002
1000 Genomes Project 30x 0.00016
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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HBA2 | - | - |
GRCh38 GRCh37 |
4 | 346 | |
LOC106804612 | - | - | - | GRCh38 | - | 283 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Hemoglobin Quong Sze
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other (1) |
no assertion criteria provided
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Mar 28, 2013 | RCV000016897.9 |
Pathogenic (2) |
no assertion criteria provided
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Jan 8, 2021 | RCV000417220.11 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Feb 16, 2024 | RCV001811168.18 | |
Pathogenic (1) |
criteria provided, single submitter
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May 9, 2022 | RCV002476982.8 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(May 09, 2022)
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criteria provided, single submitter
Method: clinical testing
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Heinz body anemia
alpha Thalassemia Hemoglobin H disease Erythrocytosis, familial, 7
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002780035.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Pathogenic
(Apr 14, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV004219830.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
Comment:
The c.377T>C (p.Leu126Pro) pathogenic variant (also known as Hb Quong Sze) is reported as being highly unstable (PMID: 6826718 (1983), 1726096 (1991)). The frequency of … (more)
The c.377T>C (p.Leu126Pro) pathogenic variant (also known as Hb Quong Sze) is reported as being highly unstable (PMID: 6826718 (1983), 1726096 (1991)). The frequency of this variant in the general population, 0.00071 (13/18322 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals who are compound heterozygous for this pathogenic variant and a large deletion that removes both of the alpha-globin genes from the alpha-globin gene cluster (e.g., the --SEA alpha-globin deletion) are reported as being affected by Hb H disease (PMID: 7070526 (1982), 7515267 (1994), 19259674 (2009)). (less)
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Pathogenic
(Oct 27, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001159864.6
First in ClinVar: Feb 10, 2020 Last updated: Feb 20, 2024 |
Comment:
The Hb Quong Sze variant (HBA2: c.377T>C; p.Leu126Pro, also known as Leu125Pro when numbered from the mature protein, rs41397847, HbVar ID: 187) is reported in … (more)
The Hb Quong Sze variant (HBA2: c.377T>C; p.Leu126Pro, also known as Leu125Pro when numbered from the mature protein, rs41397847, HbVar ID: 187) is reported in the literature in multiple Chinese individuals and families affected with alpha thalassemia (see link to HbVar and references therein). This variant has been observed in the heterozygous state in individuals with a clinical presentation resembling alpha-thalassemia trait, and in the compound heterozygous state with other pathogenic hemoglobin variants in individuals affected with hemoglobin H disease (Ahmad 2013, Goossens 1982, He 2017, Li 2011, Li 2015, Liang 1994, Liao 2009, Shang 2017, Zhou 2016). In vitro/in vivo functional analyses demonstrate that the variant protein is turned over rapidly and interferes with the formation of hemoglobin tetramers (Liebhaber 1983). This variant is reported in ClinVar (Variation ID: 15630). This variant is found in the East Asian population with an overall allele frequency of 0.08% (13/18322 alleles, including a single homozygote) in the Genome Aggregation Database. Additionally, other variants at this codon Hb West-Einde (HbVar ID: 2592), and Hb Plasencia (HbVar ID: 1226) have been reported in individuals with mild to moderate anemia, microcytosis, and hypochromia (see links to HbVar and references therein). The leucine at codon 126 is weakly conserved, but computational analyses predict that this variant is deleterious (REVEL: 0.854). Based on available information, this variant is considered to be pathogenic. References: Link to HbVar: https://globin.bx.psu.edu/hbvar/menu.html Ahmad R et al. Distribution of alpha thalassaemia gene variants in diverse ethnic populations in malaysia: data from the institute for medical research. Int J Mol Sci. 2013 Sep 10;14(9):18599-614. PMID: 24025420 Goossens M et al. Globin structural mutant alpha 125Leu leads to Pro is a novel cause of alpha-thalassaemia. Nature. 1982 Apr 29;296(5860):864-5. PMID: 7070526 He J et al. Next-generation sequencing improves thalassemia carrier screening among premarital adults in a high prevalence population: the Dai nationality, China. Genet Med. 2017 Sep;19(9):1022-1031. PMID: 28125089 Li J et al. Phenotypic variability in a chinese family with nondeletional Hb H-Hb Quong Sze disease. Hemoglobin. 2011;35(4):430-3. PMID: 21797711 Li J et al. Identification of nondeletional a-thalassemia in a prenatal screening program by reverse dot-blot in southern China. Hemoglobin. 2015;39(1):42-5. PMID: 25523870 Liang R et al. Alpha and beta thalassaemia among Chinese children in Guangxi Province, P.R. China: molecular and haematological characterization. Br J Haematol. 1994 Feb;86(2):351-4. PMID: 7515267 Liao C et al. Diversity in clinical presentation of hemoglobin H disease induced by the SEA deletion and the hemoglobin Quong Sze. Ann Hematol. 2009 Nov;88(11):1145-7. PMID: 19259674 Liebhaber SA et al. alpha-Thalassemia caused by an unstable alpha-globin mutant. J Clin Invest. 1983 Mar;71(3):461-6. PMID: 6826718 Shang X et al. Rapid Targeted Next-Generation Sequencing Platform for Molecular Screening and Clinical Genotyping in Subjects with Hemoglobinopathies. EBioMedicine. 2017 Sep;23:150-159. PMID: 28865746 Zhou JY et al. First Case of a Compound Heterozygosity for Two Nondeletional a-Thalassemia mutations, Hb Constant Spring and Hb Quong Sze. Hemoglobin. 2016 Jun;40(3):210-2. PMID: 26956449 (less)
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Pathogenic
(Feb 16, 2024)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV005325101.1
First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024 |
Comment:
Also known as Hb Quong Sze, Hb QS, p.L125P; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published … (more)
Also known as Hb Quong Sze, Hb QS, p.L125P; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies demonstrate a damaging effect and results in an unstable hemoglobin alpha molecule (PMID: 6826718); This variant is associated with the following publications: (PMID: 7070526, 34334003, 36059093, 32830468, 36900038, 26956449, 22589661, 28674233, 21797711, 1726096, 909565, 30275481, 19259674, 31553106, 25523870, 38123349, 24081251, 32811243, 28865746, 7515267, 23383304, SuwannasingS2016[Article], 32436451, 38112059, 32473995, 36685902, 24985555, 20144601, 32338097, 28125089, 11325652, Vijian2022[Review], 31111755, 24826791, WidyastitiNS2019[Article], 25352644, 6826718) (less)
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other
(Mar 28, 2013)
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no assertion criteria provided
Method: literature only
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HEMOGLOBIN QUONG SZE
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000037168.1
First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013 |
Comment on evidence:
Goossens et al. (1982) described another nondeletion mechanism: mutation in the 125th codon of the alpha-2 gene resulted in substitution of proline for leucine in … (more)
Goossens et al. (1982) described another nondeletion mechanism: mutation in the 125th codon of the alpha-2 gene resulted in substitution of proline for leucine in a region of the H helix of the alpha-globin chain, which is critical for alpha-beta contact, resulting in impediment to alpha-beta dimer formation, the initial step in hemoglobin tetramer assembly. Thus, the alpha-thalassemia phenotype results from a novel posttranslational mechanism. Goossens et al. (1982) named the mutant Quong Sze, after the province in China where the mother of their proband was born. Liang et al. (1991) reported a second example of this mutation in a Chinese family in Guangxi (Quong Sze). Hb Quong Sze is a highly unstable alpha-chain variant; because the abnormal alpha chains are rapidly catabolized, the abnormal hemoglobin is difficult to detect in reticulocytes. Identification was made through gene analysis. (less)
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Pathogenic
(Jan 08, 2021)
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no assertion criteria provided
Method: clinical testing
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Alpha thalassemia
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV002093848.1
First in ClinVar: Feb 13, 2022 Last updated: Feb 13, 2022 |
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not provided
(-)
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no classification provided
Method: literature only
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alpha Thalassemia
Affected status: unknown
Allele origin:
germline
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GeneReviews
Accession: SCV000503051.2
First in ClinVar: Mar 02, 2017 Last updated: Oct 01, 2022 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Alpha-Thalassemia. | Adam MP | - | 2024 | PMID: 20301608 |
Curating the gnomAD database: Report of novel variants in the globin-coding genes and bioinformatics analysis. | Scheps KG | Human mutation | 2020 | PMID: 31553106 |
LOVD-DASH: A comprehensive LOVD database coupled with diagnosis and an at-risk assessment system for hemoglobinopathies. | Zhang L | Human mutation | 2019 | PMID: 31286593 |
Pilot study of expanded carrier screening for 11 recessive diseases in China: results from 10,476 ethnically diverse couples. | Zhao S | European journal of human genetics : EJHG | 2019 | PMID: 30275481 |
Next-generation sequencing improves thalassemia carrier screening among premarital adults in a high prevalence population: the Dai nationality, China. | He J | Genetics in medicine : official journal of the American College of Medical Genetics | 2017 | PMID: 28125089 |
First Case of a Compound Heterozygosity for Two Nondeletional α-Thalassemia mutations, Hb Constant Spring and Hb Quong Sze. | Zhou JY | Hemoglobin | 2016 | PMID: 26956449 |
Identification of nondeletional α-thalassemia in a prenatal screening program by reverse dot-blot in southern China. | Li J | Hemoglobin | 2015 | PMID: 25523870 |
Phenotypic variability in a chinese family with nondeletional Hb H-Hb Quong Sze disease. | Li J | Hemoglobin | 2011 | PMID: 21797711 |
Diversity in clinical presentation of hemoglobin H disease induced by the SEA deletion and the hemoglobin Quong Sze. | Liao C | Annals of hematology | 2009 | PMID: 19259674 |
Alpha and beta thalassaemia among Chinese children in Guangxi Province, P.R. China: molecular and haematological characterization. | Liang R | British journal of haematology | 1994 | PMID: 7515267 |
Detection of the Hb Quong Sze mutation in a Chinese family by selective amplification of the alpha 2-globin gene and restriction map analysis with Msp I. | Liang S | Hemoglobin | 1991 | PMID: 1726096 |
alpha-Thalassemia caused by an unstable alpha-globin mutant. | Liebhaber SA | The Journal of clinical investigation | 1983 | PMID: 6826718 |
Globin structural mutant alpha 125Leu leads to Pro is a novel cause of alpha-thalassaemia. | Goossens M | Nature | 1982 | PMID: 7070526 |
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Text-mined citations for rs41397847 ...
HelpRecord last updated Nov 10, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.