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NM_000518.5(HBB):c.380T>G (p.Val127Gly) AND not provided

Germline classification:
Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:
Nov 22, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000756239.23

Allele description [Variation Report for NM_000518.5(HBB):c.380T>G (p.Val127Gly)]

NM_000518.5(HBB):c.380T>G (p.Val127Gly)

Genes:
LOC110006319:beta-globin gene 3' regulatory region [Gene]
HBB:hemoglobin subunit beta [Gene - OMIM - HGNC]
LOC107133510:origin of replication at HBB [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
11p15.4
Genomic location:
Preferred name:
NM_000518.5(HBB):c.380T>G (p.Val127Gly)
Other names:
V126G; Hb Dhonburi; Hb Neapolis; CD 126 GTG>GGG
HGVS:
  • NC_000011.10:g.5225662A>C
  • NG_000007.3:g.71954T>G
  • NG_046672.1:g.3597A>C
  • NG_053049.1:g.1983A>C
  • NG_059281.1:g.6410T>G
  • NM_000518.5:c.380T>GMANE SELECT
  • NP_000509.1:p.Val127Gly
  • LRG_1232t1:c.380T>G
  • HBB:c.380T>G
  • LRG_1232:g.6410T>G
  • LRG_1232p1:p.Val127Gly
  • NC_000011.9:g.5246892A>C
  • NM_000518.4:c.380T>G
  • P68871:p.Val127Gly
Protein change:
V127G; VAL126GLY
Links:
HBVAR: 521; UniProtKB: P68871#VAR_003056; OMIM: 141900.0393; dbSNP: rs33925391
NCBI 1000 Genomes Browser:
rs33925391
Molecular consequence:
  • NM_000518.5:c.380T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000883987ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)
Likely pathogenic
(Nov 22, 2023)
germlineclinical testing

Citation Link,

SCV001134231Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)
Pathogenic
(Jan 28, 2019)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

SCV002233194Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 16, 2023)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Hemoglobin Neapolis, beta 126(H4)Val----Gly: a novel beta-chain variant associated with a mild beta-thalassemia phenotype and displaying anomalous stability features.

Pagano L, Lacerra G, Camardella L, De Angioletti M, Fioretti G, Maglione G, de Bonis C, Guarino E, Viola A, Cutolo R, et al.

Blood. 1991 Dec 1;78(11):3070-5.

PubMed [citation]
PMID:
1954392

Compound heterozygosity for Hb Lepore-Boston and Hb Neapolis (Dhonburi) [beta 126(H4)Val-->Gly] in a patient from Naples, Italy.

Pagano L, Carbone V, Fioretti G, Viola A, Buffardi S, Rametta V, Desicato S, Pucci P, De Rosa C.

Hemoglobin. 1997 Jan;21(1):1-15.

PubMed [citation]
PMID:
9028819
See all PubMed Citations (8)

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000883987.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The Hb Dhonburi (Neapolis) variant (HBB: c.380T>G p.Val127Gly, also known as Val126Gly when numbered from the mature protein, rs33925391, HbVar ID: 521) has been reported in the heterozygous state in individuals with mild microcytosis and hypochromia (see HbVar link, Divoky 1992, Khamphikham 2022, Moghimi 2004). This variant is reported in ClinVar (Variation ID: 15483). This variant is also absent from the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. Hb Dhonburi is electrophoretically silent, but is reported to be mildly unstable in non-physiologic conditions (Bardakdjian-Michau 1990, Pagano 1991). This variant has been associated with a mild beta thalassemia phenotype with variable clinical presentation when in combination with a beta(0) HBB variant on the opposite chromosome (Bardakdjian-Michau 1990). However, an individual from the same family who was compound heterozygous for Hb E/Hb Dhonburi had hematological findings that could be explained by Hb E alone. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.67). Based on available information, the Hb Dhonburi variant is likely to be a mildly unstable structural variant and is considered likely pathogenic. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Bardakdjian-Michau J et al. Hemoglobin Dhonburi alpha 2 beta 2 126 (H4) Val----Gly: a new unstable beta variant producing a beta-thalassemia intermedia phenotype in association with beta zero-thalassemia. Am J Hematol. 1990 Oct;35(2):96-9. PMID: 2399911. Divoky V et al. Heterozygosity for the IVS-I-5 (G-->C) mutation with a G-->A change at codon 18 (Val-->Met; Hb Baden) in cis and a T-->G mutation at codon 126 (Val-->Gly; Hb Dhonburi) in trans resulting in a thalassemia intermedia. Biochim Biophys Acta. 1992 Dec 10;1180(2):173-9. PMID: 1463768. Khamphikham P et al. Strong Positive Dichlorophenolindophenol Precipitation Suggests Hb Dhonburi (or Hb Neapolis) (HBB: c.380T>G) Inheritance in a Couple at Risk for Severe ß-Thalassemia. Hemoglobin. 2022 May;46(3):184-186. PMID: 35543019. Moghimi B et al. Hb Dhonburi (Neapolis) [beta126(H4)Val-->Gly] identified in a family from northern Iran. Hemoglobin. 2004;28(4):353-6. PMID: 15658193. Pagano L et al. Hemoglobin Neapolis, beta 126(H4)Val----Gly: a novel beta-chain variant associated with a mild beta-thalassemia phenotype and displaying anomalous stability features. Blood. 1991 Dec 1;78(11):3070-5. PMID: 1954392.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001134231.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

The best available variant frequency is uninformative. Found in at least one symptomatic patient. Occurs in multiple cases with a recessive pathogenic variant in the same gene. Assessment of experimental evidence suggests this variant results in abnormal protein function.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV002233194.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 15483). This variant is also known as Hb Dhonburi, Hb Neapolis and p.Val126Gly. This missense change has been observed in individual(s) with thalassemia intermedia (PMID: 1463768, 17007829). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces valine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 127 of the HBB protein (p.Val127Gly).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 9, 2024