NM_000184.3:c.190C>T

Variant names:

• chr11-5254417-G-A
• rs34474104
• NM_000184.3:c.190C>T

Variant summary

Our verdict is Pathogenic. The variant received 16 ACMG points: 16P and 0B. PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000184.3(HBG2):​c.190C>T​(p.His64Tyr) variant causes a missense change. 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H64L) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 31)
• Consequence: HBG2 NM_000184.3 missense
• Clinical Significance: Likely pathogenic criteria provided, multiple submitters, no conflicts P:3
• Conservation: PhyloP100: 6.38
• Publications: 9 publications found

Genes affected

HBG2 (HGNC:4832): (hemoglobin subunit gamma 2) The gamma globin genes (HBG1 and HBG2) are normally expressed in the fetal liver, spleen and bone marrow. Two gamma chains together with two alpha chains constitute fetal hemoglobin (HbF) which is normally replaced by adult hemoglobin (HbA) at birth. In some beta-thalassemias and related conditions, gamma chain production continues into adulthood. The two types of gamma chains differ at residue 136 where glycine is found in the G-gamma product (HBG2) and alanine is found in the A-gamma product (HBG1). The former is predominant at birth. 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]

HBG2 Gene-Disease associations (from GenCC):

• hemoglobinopathy Toms River

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary persistence of fetal hemoglobin-beta-thalassemia syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary persistence of fetal hemoglobin-sickle cell disease syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• cyanosis, transient neonatal

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000284931 (HGNC:):

ACMG classification

Our verdict: Pathogenic. The variant received 16 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-5254416-T-A is described in ClinVar as Pathogenic. ClinVar VariationId is 29752.Status of the report is no_assertion_criteria_provided, 0 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.989
• PP5: Variant 11-5254417-G-A is Pathogenic according to our data. Variant chr11-5254417-G-A is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 14981.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HBG2	NM_000184.3	c.190C>T	p.His64Tyr	missense_variant	Exon 2 of 3	ENST00000336906.6	NP_000175.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HBG2	ENST00000336906.6	c.190C>T	p.His64Tyr	missense_variant	Exon 2 of 3	1	NM_000184.3	ENSP00000338082.4
ENSG00000284931	ENST00000642908.1	c.190C>T	p.His64Tyr	missense_variant	Exon 2 of 3			ENSP00000495346.1
ENSG00000239920	ENST00000380259.7	n.*1493C>T		non_coding_transcript_exon_variant	Exon 8 of 8	5		ENSP00000369609.3
ENSG00000239920	ENST00000380259.7	n.*1493C>T		3_prime_UTR_variant	Exon 8 of 8	5		ENSP00000369609.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Nov 06, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Hb F-M-Osaka variant (HBG2: c.190C>T; p.His64Tyr, also known as His63Tyr when numbered from the mature protein, rs34474104, HbVar ID: 601) has been reported in newborns with mild methemoglobinemia and transient neonatal cyanosis (Alonso-Ojembarrena 2016, Chandran 2022, Chen 2024, Yuan 2020, see HbVar and references therein). Hb F-M-Osaka has also been found to segregate with transient neonatal cyanosis (Alonso-Ojembarrena 2016, Yuan 2020). This variant is absent from the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.88). Based on available information, this variant is considered to be likely pathogenic. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Alonso-Ojembarrena A et al. Hemoglobin M Disease as a Cause of Cyanosis in a Newborn. J Pediatr Hematol Oncol. 2016 Apr;38(3):173-5. PMID: 26694193. Chandran S et al. The journey from blue to pink–a rare cause for self-limiting methemoglobinemia in an Indian baby. Case Reports in Perinatal Medicine. 2022 Aug 11. https://doi.org/10.1515/crpm-2021-0054 Chen Y et al. Case Report: A case report and literature review of hemoglobin variation associated with neonatal cyanosis. Front Pediatr. 2024 Feb 13;12:1334757. PMID: 38415208. Yuan J and Zhu XP. Clinical characteristics on manifestation and gene mutation of a transient neonatal cyanosis: A case report. World J Clin Cases. 2020 Jan 6;8(1):217-221. PMID: 31970190. -

May 17, 2024

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as Hb FM-Osaka and p.(H63Y); This variant is associated with the following publications: (PMID: 19065339, 2470018, 38415208, 6158500, 8811323, Chandran2022[CaseReport], 31970190, 12603090) -

Cyanosis, transient neonatal Pathogenic:1

Jan 01, 2008

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.91
BayesDel_addAF	Pathogenic	0.48	D
BayesDel_noAF	Pathogenic	0.45
CADD	Benign	20
DANN	Uncertain	1.0
DEOGEN2	Benign	0.29	.;.;T;.
Eigen	Uncertain	0.30
Eigen_PC	Uncertain	0.26
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.91	D;D;D;D
M_CAP	Uncertain	0.21	D
MetaRNN	Pathogenic	0.99	D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.5	.;.;H;.
PhyloP100		6.4
PROVEAN	Pathogenic	-5.7	.;.;D;.
REVEL	Pathogenic	0.88
Sift	Uncertain	0.013	.;.;D;.
Sift4G	Uncertain	0.0050	.;.;D;.
Polyphen		0.15	.;.;B;.
Vest4		0.68
MutPred		0.96		Loss of disorder (P = 0.0351);Loss of disorder (P = 0.0351);Loss of disorder (P = 0.0351);.;
MVP		0.93
ClinPred		0.88	D
GERP RS		3.9
PromoterAI		-0.0020	Neutral
RBP_binding_hub_radar		1.1
RBP_regulation_power_radar		2.3
Varity_R		0.71
gMVP		0.96
Mutation Taster		=2/98	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs34474104; hg19: chr11-5275647; COSMIC: COSV108150192; COSMIC: COSV108150192;