11-5225611-T-G

Position:

• chr11-5225611-T-G

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1 PM2 PM5 PP3 PP5_Moderate

The NM_000518.5(HBB):​c.431A>C​(p.His144Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic 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. H144?) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 33)
• Consequence: HBB NM_000518.5 missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:2 O:1
• Conservation: PhyloP100: 0.519

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 9 ACMG points.

• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 10 uncertain in NM_000518.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-5225611-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 15090.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.839
• PP5: Variant 11-5225611-T-G is Pathogenic according to our data. Variant chr11-5225611-T-G is described in ClinVar as [Pathogenic]. Clinvar id is 15365.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HBB	NM_000518.5	c.431A>C	p.His144Pro	missense_variant	3/3	ENST00000335295.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBB	ENST00000335295.4	c.431A>C	p.His144Pro	missense_variant	3/3	1	NM_000518.5	P1
HBB	ENST00000647020.1	c.431A>C	p.His144Pro	missense_variant	3/3			P1
HBB	ENST00000633227.1	c.*247A>C		3_prime_UTR_variant, NMD_transcript_variant	3/3	3
HBB	ENST00000475226.1			downstream_gene_variant		2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2 Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Jun 20, 2019

The Hb Syracuse variant (HBB: c.431A>C; p.His144Pro, also known as His143Pro when numbered from the mature protein; rs33918338) is reported in the literature in the heterozygous state in several individuals affected with erythrocytosis (Gonzalez Fernandez 2009, Jensen 1975, HbVar database). At least one individual with this variant had multiple family members with erythrocytosis (Jensen 1975), and its occurrence in heterozygous affected individuals suggests it acts in a dominant manner (Gonzalez Fernandez 2009, Jensen 1975, HbVar database). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The histidine at codon 144 is highly conserved, occurs in the functionally important 2,3-diphosphoglycerate binding site (Wajcman 2005), and functional studies indicate this variant exhibits increased oxygen affinity (Jensen 1975). Additionally, other amino acid substitutions at this codon (p.His144Gln, p.His144Arg) exhibit increased oxygen affinity and are associated with erythrocytosis (Camps 2016, Venkateswaran 2005, Wajcman 2005). Based on available information, the Hb Syracuse variant is considered to be pathogenic. References: HbVar link for Hb Syracuse: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=564 Camps C et al. Gene panel sequencing improves the diagnostic work-up of patients with idiopathic erythrocytosis and identifies new mutations. Haematologica. 2016 Nov;101(11):1306-1318. Gonzalez Fernandez FA et al. Haemoglobinopathies with high oxygen affinity. Experience of Erythropathology Cooperative Spanish Group. Ann Hematol. 2009 Mar;88(3):235-8. Jensen M et al. Hemoglobin Syracuse (alpha2beta2-143(H21)His leads to Pro), a new high-affinity variant detected by special electrophoretic methods. Observations on the auto-oxidation of normal and variant hemoglobins. J Clin Invest. 1975 Mar;55(3):469-77. Venkateswaran L et al. Homozygous hemoglobin Abruzzo in a North American child. J Pediatr Hematol Oncol. 2005 Nov;27(11):618-20. Wajcman H and Galacteros F. Hemoglobins with high oxygen affinity leading to erythrocytosis. New variants and new concepts. Hemoglobin. 2005;29(2):91-106. -

Erythrocytosis, familial, 6 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 01, 1975

- -

HEMOGLOBIN SYRACUSE 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	Pathogenic	0.86
BayesDel_addAF	Pathogenic	0.43	D
BayesDel_noAF	Pathogenic	0.38
CADD	Benign	23
DANN	Benign	0.96
DEOGEN2	Benign	0.12	T;T
Eigen	Uncertain	0.31
Eigen_PC	Uncertain	0.31
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.81	.;T
M_CAP	Pathogenic	0.63	D
MetaRNN	Pathogenic	0.84	D;D
MetaSVM	Pathogenic	0.80	D
MutationAssessor	Uncertain	2.8	M;M
MutationTaster	Benign	0.97	D
PrimateAI	Benign	0.40	T
PROVEAN	Uncertain	-4.3	D;.
REVEL	Pathogenic	0.79
Sift	Pathogenic	0.0	D;.
Sift4G	Benign	0.068	T;.
Polyphen		0.76	P;P
Vest4		0.75
MutPred		0.59		Loss of MoRF binding (P = 0.0707);Loss of MoRF binding (P = 0.0707);
MVP		0.96
MPC		0.045
ClinPred		0.98	D
GERP RS		4.7
Varity_R		0.88
gMVP		0.92

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs33918338; hg19: chr11-5246841;