11-5225678-C-G

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 12P and 5B. PM1 PM5 PP5_Very_Strong BP4 BS2

The NM_000518.5(HBB):c.364G>C(p.Glu122Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000444 in 1,614,096 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E122A) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00022 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00047 (8 hom.)
• Consequence: HBB NM_000518.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:15 O:2
• Conservation: PhyloP100: 4.94

Genes affected

HBB (HGNC:4827): (hemoglobin subunit beta) The alpha (HBA) and beta (HBB) loci determine the structure of the 2 types of polypeptide chains in adult hemoglobin, Hb A. The normal adult hemoglobin tetramer consists of two alpha chains and two beta chains. Mutant beta globin causes sickle cell anemia. Absence of beta chain causes beta-zero-thalassemia. Reduced amounts of detectable beta globin causes beta-plus-thalassemia. The order of the genes in the beta-globin cluster is 5'-epsilon -- gamma-G -- gamma-A -- delta -- beta--3'. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

• PM1: In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 4 benign, 15 uncertain in NM_000518.5
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-5225678-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 15292.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP5: Variant 11-5225678-C-G is Pathogenic according to our data. Variant chr11-5225678-C-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 15152.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-5225678-C-G is described in Lovd as [Pathogenic]. Variant chr11-5225678-C-G is described in Lovd as [Likely_pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.017982274).. Strength limited to SUPPORTING due to the PP5.
• BS2: High Homozygotes in GnomAdExome at 4 AD,AR,Digenic gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HBB	NM_000518.5	c.364G>C	p.Glu122Gln	missense_variant	3/3	ENST00000335295.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBB	ENST00000335295.4	c.364G>C	p.Glu122Gln	missense_variant	3/3	1	NM_000518.5	P1
HBB	ENST00000647020.1	c.364G>C	p.Glu122Gln	missense_variant	3/3			P1
HBB	ENST00000475226.1	n.296G>C		non_coding_transcript_exon_variant	2/2	2
HBB	ENST00000633227.1	c.*180G>C		3_prime_UTR_variant, NMD_transcript_variant	3/3	3

Frequencies

GnomAD3 genomes AF: 0.000223 AC: 34 AN: 152170 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00435

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000696 AC: 175 AN: 251306 Hom.: 4 AF XY: 0.00104 AC XY: 141 AN XY: 135810

Gnomad AFR exome AF: 0.0000615

Gnomad AMR exome AF: 0.0000867

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00500

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000132

Gnomad OTH exome AF: 0.000490

GnomAD4 exome AF: 0.000467 AC: 683 AN: 1461808 Hom.: 8 Cov.: 31 AF XY: 0.000623 AC XY: 453 AN XY: 727214

Gnomad4 AFR exome AF: 0.0000597

Gnomad4 AMR exome AF: 0.000112

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00507

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000185

Gnomad4 OTH exome AF: 0.000364

GnomAD4 genome AF: 0.000223 AC: 34 AN: 152288 Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23 AN XY: 74474

Gnomad4 AFR AF: 0.0000722

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00435

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000147

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000890 Hom.: 0

Bravo AF: 0.000106

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000519 AC: 2

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000233 AC: 2

ExAC AF: 0.000700 AC: 85

Asia WGS AF: 0.00144 AC: 5 AN: 3478

EpiCase AF: 0.000327

EpiControl AF: 0.0000593

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:15Other:2

Revision: criteria provided, multiple submitters, no conflicts

LINK:

Submissions by phenotype

not provided Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 23, 2022	Considered a founder mutation with prevalence in the Punjabi region of India, Italy, Belgium, Austria, and Turkey (Torres Lde et al., 2015); Also referred to as E121Q due to the use of alternative nomenclature, and commonly called HbD Punjab or HbD Los Angeles (Torres Lde S et al., 2015); Published functional studies suggest a damaging effect, including decreased oxygen affinity of HbD (Narayanan et al., 2020); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 3557998, 25087612, 22975760, 19958184, 25666204, 24123366, 22028795, 2307460, 26680249, 26990548, 8095930, 12403491, 24616059, 2895770, 20110664, 5672850, 4078867, 21194265, 25818823, 24814631, 28970692, 9140717, 30626242, 31553106, 31973650, 31980526, 34426522, 33867742, 6592161, 10490135, 32468185, 1177278) -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Feb 11, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 21, 2023	The Hb D-Los Angeles variant (HBB: c.364G>C; p.Glu122Gln, also known as Glu121Gln when numbered from the mature protein, HbVar ID: 509) is not associated with clinical symptoms in heterozygous carriers (HbVar database). Individuals homozygous for Hb D-Los Angeles are also commonly clinically asymptomatic (HbVar database, Torres 2015). Individuals with Hb D-Los Angeles who carry an additional pathogenic variant in their other copy of the beta globin gene may have clinically significant symptoms. Hb D-Los Angeles paired with HbS has a wide phenotypic spectrum ranging from mild to severe sickle cell disease (Perea 1999, Torres 2015 and 2016). Functional studies found an increased rate of nucleation and polymerization in Hb S- D Los Angeles samples as compared with Hb S (Adachi 1988). The clinical presentation in individuals with Hb D-Los Angeles and a beta-thalassemia variant is variable and influenced by the severity of the thalassemia variant, but is commonly characterized by mild to moderate hemolytic anemia (Perea 1999, Theodoridou 2009, Torres 2015 and 2016). This variant is reported in ClinVar (Variation ID: 15152) and is found in the South Asian population with an allele frequency of 0.5% (153/30616 alleles, including 4 homozygotes) in the Genome Aggregation Database. Based on available information, this variant is considered to be pathogenic. REFERENCES Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Adachi K et al. Facilitation of Hb S polymerization by the substitution of Glu for Gln at beta 121. J Biol Chem. 1988 Apr 25;263(12):5607-10. PMID: 2895770. Perea F et al. Hb D-Los Angeles associated with Hb S or beta-thalassemia in four Mexican Mestizo families. Hemoglobin. 1999; 23(3):231-7. PMID: 10490135. Theodoridou S et al. Compound heterozygosity for Hb D-Punjab / beta-thalassemia and blood donation: case report. Turk J Haematol. 2009 Jun 5;26(2):100-1. PMID: 27265282. Torres LS et al. Hemoglobin D-Punjab: origin, distribution and laboratory diagnosis. Rev Bras Hematol Hemoter. 2015 Mar-Apr;37(2):120-6. PMID: 25818823. Torres LS et al. Phenotypic Diversity of Sickle Cell Disease in Patients with a Double Heterozygosity for Hb S and Hb D-Punjab. Hemoglobin. 2016 Sep;40(5):356-358. PMID: 27535451. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jan 09, 2023	In the published literature, individuals who are heterozygous or homozygous for this variant typically have a normal clinical presentation (PMIDs: 30626242 (2018), 25666204 (2015), 24123366 (2014), 12403491 (2002), and 1177278 (1975)). There have been individuals reported to have mild anemia when compound heterozygous with additional HBB variants (PMIDs: 31973650 (2020), 9140717 (1997), and 4078867 (1985)). However, individuals who are compound heterozygous for the Hb D-Los Angeles and Hb S variants have a clinically significant sickling disorder that is similar to sickle cell disease (PMIDs: 25818823 (2015), 24616059 (2014), and 5672850 (1968)). Additionally, individuals who are compound heterozygous for the Hb D-Los Angeles variant and a beta-globin pathogenic variant associated with beta-thalassemia may be affected by beta-thalassemia (PMID: 30626242 (2018), 25087612 (2014), 22028795 (2011), 2307460 (1990)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is deleterious or benign. Based on the available information, this variant is classified as likely pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 29, 2024	This sequence change replaces glutamic acid, which is acidic and polar, with glutamine, which is neutral and polar, at codon 122 of the HBB protein (p.Glu122Gln). This variant is present in population databases (rs33946267, gnomAD 0.5%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individuals with an HbSD phenotype, which occurs when this variant is co-inherited with HBB p.Glu7Val (also known as p.Glu6Val and HbS). HbSD is a moderate to severe phenotype similar to that seen in sickle cell anemia. When observed in the heterozygous or homozygous state, this variant is generally asymptomatic. (PMID: 24245819, 24616059, 25666204). This variant is also known as p.Glu121Gln, HbD-Los Angeles, HbD-Punjab, HbD-North-Carolina, HbD-Portugal, and HbD-Chicago. ClinVar contains an entry for this variant (Variation ID: 15152). 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: 2895770). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	Mar 01, 2018	- -

beta Thalassemia Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Knight Diagnostic Laboratories, Oregon Health and Sciences University	Jan 27, 2016	The c.346G>C (p.Glu534Gln) missense variant, Hb D-Los Angeles, is the fourth most common hemoglobin variant world-wide. Multiple reports identify the variant as pathogenic in combination with Hb S. Co-inheritance of Hb D-Los Angeles with Hb S results in Hb SD-Los Angeles (compound heterozygotes) and a moderate to severe clinical phenotype similar to that of sickle cell anemia (SCA). Patients with Hb SD disease have severe hemolytic anemia and recurrent vaso-occlusive episodes. Hb S molecules undergo two-step process leading to nucleation and ultimately the formation of a complex sickle polymer in the deoxygenated state. It is proposed that in the Hb SD-Los Angeles molecule, the Glu122Gln substitution strengthens the second step thereby accelerating polymerization. Thus the Hb D-Los Angeles genotype might increases the probability of sickling (GeneReviews: Origa, 2015, http://www.ncbi.nlm.nih.gov/books/NBK1426/, GeneReviews: Bender et al., 2014, http://www.ncbi.nlm.nih.gov/books/NBK1377/). This missense variant has significantly increased prevalence in affected individuals relative to controls. Individuals who are either heterozygous or homozygous for the Hb D-Los Angeles variant alone are generally asymptomatic, although rarely, Hb D homozygous individuals can present with mild hemolytic anemia and mild to moderate splenomegaly (GeneReviews: Origa, 2015, http://www.ncbi.nlm.nih.gov/books/NBK1426/, GeneReviews: Bender et al., 2014, http://www.ncbi.nlm.nih.gov/books/NBK1377/). Therefore, this collective evidence supports the classification of the c.364G>C (p.Glu122Gln) as a Pathogenic variant for Beta Thalassemia. -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 03, 2022	The p.Glu122Gln variant in HBB (also known as Glu121Gln, HbD-Los Angeles, HbD-Punjab, HbD-North-Carolina, HbD-Portugal, and HbD-Chicago) is considered a founder mutation in the Punjabi region of India, Italy, Belgium, Austria, and Turkey (Torres Lde 2015 PMID: 25818823). Heterozygous carriers, but also homozygous individuals, are commonly clinically asymptomatic (HbVar database, Torres Lde 2015 PMID: 25818823). However, individuals who carry this variant in trans with another pathogenic variant may have clinically significant symptoms e.g., sickle cell disease or hemolytic anemia (Perea 1999 PMID: 10490135, Theodoridou 2009 PMID: 27265282, Torres Lde 2015 PMID: 25818823). This variant has also been reported in ClinVar (Variation ID 15152). It has been identified in 21/4828 South Asian and in 10/68032 European chromosomes by gnomAD (https://gnomad.broadinstitute.org/). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In vitro functional studies support an impact on protein function (Adachi 1988 PMID: 2895770). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive hemoglobinopathy. ACMG/AMP Criteria applied: PM3_VS, PS3_Moderate. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Oct 18, 2019	NM_000518.4(HBB):c.364G>C(E122Q, aka Hb D-Punjab) is classified as likely pathogenic in the context of Hb beta chain-related hemoglobinopathy. Sources cited for classification include the following: PMID 5672850, 3557998, 4078867 and 1177278. Classification of NM_000518.4(HBB):c.364G>C(E122Q, aka Hb D-Punjab) 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 -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Mar 17, 2017	- -

Hb SS disease Pathogenic:2Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	May 18, 2021	- -
not provided, no classification provided	literature only	GeneReviews	-	- -

Heinz body anemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Mendelics

May 04, 2022

- -

HBB-Related Disorders Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2019

The HBB c.364G>C (p.Glu122Gln) missense variant, which is also reported as p.Glu121Gln, Hb D-Punjab, and Hb D-Los Angeles, is the fourth most common haemoglobin variant found worldwide. Individuals who carry this variant in a heterozygous or homozygous state are generally asymptomatic, however, inheritance in a homozygous can result in a mild to moderate hemolytic anemia (Taghavi Basmanj et al. 2011; Torres et al. 2015). The p.Glu122Gln variant can occur in association with other hemoglobin variants, for example, HbS or thalassemia, resulting in moderate to severe clinical manifestations resembling a sickle cell disease phenotype or a mild microcytic and hypochromic anemia respectively (Adekile et al. 2010; Bender et al. 2014; Torres et al. 2015). The variant is reported at a frequency of 0.004997 in the South Asian population of the Genome Aggregation Database. Based on the evidence the p.Glu122Gln variant is classified as likely pathogenic for HBB-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -

Hemoglobin D disease Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Oct 18, 2019

Variant summary: HBB c.364G>C (p.Glu122Gln) results in a conservative amino acid change in the encoded protein sequence and is a common disease-associated variant. The variant is also cited in the literature as HbD-Los Angeles, HbD-Punjab, HbD-North-Carolina, HbD-Portugal, and HbD-Chicago. 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 0.0007 in 251306 control chromosomes in the gnomAD database, including 4 homozygotes. When found in a homozygous or heterozygous state, c.364G>C is typically associated with either no disease phenotype or very mild anemia (e.g. Politis-Tsegos_1975, Rahimi_2006). However, when found in trans with other thalassemia-associated variants, phenotypes can range from mild to severe anemias and splenomegaly (e.g. Worthington_1985, Fucharoen_2002, Rahimi_2006). In addition, patients with this variant in trans with a pathogenic Hgb S variant may have a severe phenotype similar to Sickle Cell Disease (e.g. Mukherjee_2005). These data indicate that the variant is very likely to be associated with disease. At least one study has reported that the p.Glu122Gln protein may facilitate polymerization of Hgb S (Adachi_1998). Seven other laboratories have submitted clinical-significance assessments for this variant to ClinVar (evaluation after 2014), citing the variant four times as pathogenic, two times as likely pathogenic, and one time as uncertain significance. Based on the evidence outlined above, the variant was classified as pathogenic. -

Hb D-Los Angeles Other:1

other, no assertion criteria provided

literature only

OMIM

Dec 12, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Uncertain

0.093

D

BayesDel_noAF

Pathogenic

0.36

Cadd

Benign

21

Dann

Uncertain

0.98

DEOGEN2

Benign

0.027

T;T

Eigen

Benign

-0.067

Eigen_PC

Benign

-0.068

FATHMM_MKL

Uncertain

0.90

D

M_CAP

Uncertain

0.23

D

MetaRNN

Benign

0.018

T;T

MetaSVM

Uncertain

0.28

D

MutationAssessor

Pathogenic

3.0

M;M

MutationTaster

Benign

1.0

N

PrimateAI

Benign

0.37

T

PROVEAN

Benign

-1.7

N;.

REVEL

Uncertain

0.57

Sift

Uncertain

0.0060

D;.

Sift4G

Benign

0.11

T;.

Polyphen

0.17

B;B

Vest4

0.51

MVP

0.99

MPC

0.034

ClinPred

0.063

T

GERP RS

4.7

Varity_R

0.33

gMVP

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs33946267; hg19: chr11-5246908; COSMIC: COSV58941641; COSMIC: COSV58941641;