HBG1

hemoglobin subunit gamma 1, the group of Hemoglobin subunits

Basic information

Region (hg38): 11:5248269-5249857

Links

ENSG00000213934 ∙ NCBI:3047 ∙ OMIM:142200 ∙ HGNC:4831 ∙ Uniprot:P69891 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hereditary persistence of fetal hemoglobin-beta-thalassemia syndrome (Supportive), mode of inheritance: AD
• delta-beta-thalassemia (Supportive), mode of inheritance: AR
• hereditary persistence of fetal hemoglobin-sickle cell disease syndrome (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hereditary persistence of fetal hemoglobin	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Hematologic	2578620; 2423160; 21057501

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HBG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HBG1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			4	7	2	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		6	7
Total	0	0	5	7	8

Variants in HBG1

This is a list of pathogenic ClinVar variants found in the HBG1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-5248352-AG-A		HBG1-related disorder	Benign (Oct 31, 2019)
11-5248353-G-A		Hereditary persistence of fetal hemoglobin	Benign (Sep 28, 2023)
11-5248354-T-G		Hereditary persistence of fetal hemoglobin	Benign (Sep 28, 2023)
11-5248355-G-A		Hereditary persistence of fetal hemoglobin	Benign (Sep 28, 2023)
11-5248356-A-G		Hereditary persistence of fetal hemoglobin	Benign (Sep 28, 2023)
11-5248356-A-AG		HBG1-related disorder	Benign (Oct 31, 2019)
11-5248378-A-G		not specified	Uncertain significance (Mar 28, 2023)
11-5248393-G-C		Hereditary persistence of fetal hemoglobin	Benign (Jan 21, 2022)
11-5248394-C-A		-	no classification for the single variant (-)
11-5248400-C-T		HEMOGLOBIN F (JIANGSU)	other (Jul 15, 2011)
11-5248418-C-T		HEMOGLOBIN F (BASKENT)	other (Jul 15, 2011)
11-5248426-T-G		Hereditary persistence of fetal hemoglobin	Likely benign (Jan 21, 2022)
11-5248436-A-G		not specified	Uncertain significance (Feb 28, 2024)
11-5248439-C-T		HEMOGLOBIN F (SIENA) • HEMOGLOBIN F (HULL) • Fetal hemoglobin quantitative trait locus 1	Likely benign (Oct 21, 2021)
11-5249390-T-A		not specified	Uncertain significance (Mar 14, 2023)
11-5249390-T-C		HEMOGLOBIN F (DICKINSON)	other (Jul 15, 2011)
11-5249442-C-A		HEMOGLOBIN F (VICTORIA JUBILEE)	other (Jul 15, 2011)
11-5249442-C-T		HEMOGLOBIN F (YAMAGUCHI)	other (Jul 15, 2011)
11-5249445-C-T		HEMOGLOBIN F (DAMMAM)	other (Jan 01, 1985)
11-5249456-G-A		HBG1 POLYMORPHISM • HEMOGLOBIN F (SARDINIA) • not specified • Hereditary persistence of fetal hemoglobin	Benign (Apr 20, 2022)
11-5249463-C-G		HEMOGLOBIN F (XIN-SU)	other (Jul 15, 2011)
11-5249463-C-T		HEMOGLOBIN F (FOREST PARK)	other (Jul 15, 2011)
11-5249466-C-G		HEMOGLOBIN F (IWATA)	other (Jul 15, 2011)
11-5249466-C-T		Hereditary persistence of fetal hemoglobin	Likely benign (Apr 01, 2022)
11-5249499-T-C		HEMOGLOBIN F (JAMAICA)	other (Jul 15, 2011)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HBG1	protein_coding	protein_coding	ENST00000330597	3	1810

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.566	0.390	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.780	40	56.5	0.708	0.00000258	948
Missense in Polyphen		9	16.447	0.54721		314
Synonymous	2.10	11	24.1	0.456	0.00000119	291
Loss of Function	1.48	0	2.55	0.00	1.08e-7	49

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Gamma chains make up the fetal hemoglobin F, in combination with alpha chains.
• Pathway: ATF-2 transcription factor network (Consensus)

Recessive Scores

• pRec: 0.783

Haploinsufficiency Scores

• pHI: 0.513
• hipred: N
• hipred_score: 0.238
• ghis: 0.967

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.387

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Medium
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: blood coagulation;oxygen transport;hydrogen peroxide catabolic process;protein heterooligomerization;cellular oxidant detoxification
• Cellular component: cytosol;hemoglobin complex;haptoglobin-hemoglobin complex
• Molecular function: peroxidase activity;oxygen carrier activity;protein binding;oxygen binding;heme binding;haptoglobin binding;organic acid binding;metal ion binding