HBD

hemoglobin subunit delta, the group of Hemoglobin subunits

Basic information

Region (hg38): 11:5232678-5243657

Links

ENSG00000223609 ∙ NCBI:3045 ∙ OMIM:142000 ∙ HGNC:4829 ∙ Uniprot:P02042 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• delta-beta-thalassemia (Supportive), mode of inheritance: AR

ClinVar

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

• not provided (3 variants)
• alpha Thalassemia (1 variants)
• Hemoglobin Lepore trait (1 variants)
• HEMOGLOBIN A(2) BABINGA (1 variants)
• delta Thalassemia (1 variants)
• Anemia;Abnormal hemoglobin;Persistence of hemoglobin F;Reduced beta/alpha synthesis ratio (1 variants)
• Delta-beta-thalassemia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HBD 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			4	1	1	6
missense	1		10			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region						0
non coding	1		6		3	10
Total	3	0	20	1	4

Highest pathogenic variant AF is 0.000768

Variants in HBD

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

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

Position	Type	Phenotype	Significance	ClinVar
11-5232765-C-T		delta Thalassemia	Pathogenic (Jan 15, 1992)
11-5232862-C-T		HBD-related disorder	Uncertain significance (Nov 21, 2017)
11-5232868-C-A		Fetal hemoglobin quantitative trait locus 1	Uncertain significance (Jan 13, 2018)
11-5232873-C-T		Fetal hemoglobin quantitative trait locus 1	Uncertain significance (Jan 13, 2018)
11-5232899-A-G		Fetal hemoglobin quantitative trait locus 1	Uncertain significance (Jan 13, 2018)
11-5232905-G-C		Fetal hemoglobin quantitative trait locus 1	Uncertain significance (Jan 13, 2018)
11-5232968-T-C		HEMOGLOBIN A(2) MONREALE	other (Dec 12, 2017)
11-5232971-T-A		not specified	Uncertain significance (Oct 26, 2022)
11-5232980-G-T		HEMOGLOBIN A(2) FITZROY	other (Dec 12, 2017)
11-5232983-A-G		HEMOGLOBIN A(2) PELENDRI	other (Dec 12, 2017)
11-5232984-G-C		not specified	Uncertain significance (May 27, 2022)
11-5232998-C-T		HEMOGLOBIN A(2) BABINGA	Pathogenic (Jul 26, 2022)
11-5233007-A-G		HEMOGLOBIN A(2) NINIVE	other (Dec 12, 2017)
11-5233032-G-C		HEMOGLOBIN A(2) ZAGREB	other (Dec 12, 2017)
11-5233043-T-A		HEMOGLOBIN A(2) MANZANARES	other (Dec 12, 2017)
11-5233045-C-T		HBD-related disorder	Likely benign (Jul 15, 2019)
11-5233058-C-T		HEMOGLOBIN A(2) COBURG	other (Dec 12, 2017)
11-5233059-G-A		HEMOGLOBIN A(2) TROODOS • HEMOGLOBIN A(2) CORFU	other (Dec 12, 2017)
11-5233076-A-G		Thalassemia	Uncertain significance (Jan 23, 2023)
11-5233094-T-C		delta Thalassemia	Pathogenic (Jun 12, 2019)
11-5233097-G-A		HBD-related disorder	Uncertain significance (Jan 05, 2021)
11-5233845-A-C			Benign (Jun 20, 2021)
11-5233985-A-T		delta Thalassemia	Pathogenic (Feb 01, 2002)
11-5233991-C-A		HEMOGLOBIN A(2) CAPRI	other (Dec 12, 2017)
11-5234008-C-T		HEMOGLOBIN A(2) CANADA	other (Dec 12, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HBD	protein_coding	protein_coding	ENST00000380299	3	2693

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000192	0.156	125716	0	21	125737	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.01	99	74.4	1.33	0.00000365	956
Missense in Polyphen		30	21.824	1.3746		336
Synonymous	-0.884	36	29.9	1.21	0.00000142	299
Loss of Function	-0.966	6	3.93	1.53	1.69e-7	49

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in oxygen transport from the lung to the various peripheral tissues.

Intolerance Scores

• loftool: 0.138
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.04

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.334

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	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;blood microparticle
• Molecular function: peroxidase activity;oxygen carrier activity;protein binding;oxygen binding;heme binding;haptoglobin binding;hemoglobin alpha binding;organic acid binding;metal ion binding