GeneBe

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_specified (12 variants)
  • not_provided (9 variants)
  • Fetal_hemoglobin_quantitative_trait_locus_1 (7 variants)
  • delta_Thalassemia (5 variants)
  • Hemoglobin_Lepore_trait (4 variants)
  • Thalassemia (4 variants)
  • HBD-related_disorder (3 variants)
  • Delta-0-thalassemia (2 variants)
  • HEMOGLOBIN_A(2)_INDONESIA (1 variants)
  • HEMOGLOBIN_A(2)_PUGLIA (1 variants)
  • HEMOGLOBIN_A(2)_YIALOUSA (1 variants)
  • HEMOGLOBIN_A(2)_PARKVILLE (1 variants)
  • HEMOGLOBIN_A(2)_GROVETOWN (1 variants)
  • HEMOGLOBIN_A(2)_CAMPANIA (1 variants)
  • Glucocorticoid-remediable_aldosteronism (1 variants)
  • HEMOGLOBIN_A(2)_NIIGATA (1 variants)
  • HEMOGLOBIN_A(2)_HONAI (1 variants)
  • HEMOGLOBIN_A(2)_FLATBUSH (1 variants)
  • HEMOGLOBIN_A(2)_BABINGA (1 variants)
  • HEMOGLOBIN_A(2)_COBURG (1 variants)
  • HEMOGLOBIN_A(2)_SPHAKIA (1 variants)
  • HEMOGLOBIN_A(2)_NINIVE (1 variants)
  • HEMOGLOBIN_A(2)_YOKOSHIMA (1 variants)
  • HEMOGLOBIN_A(2)_ROOSEVELT (1 variants)
  • HEMOGLOBIN_A(2)_PELENDRI (1 variants)
  • HEMOGLOBIN_A(2)_ZAGREB (1 variants)
  • HEMOGLOBIN_A(2)_AGRINIO (1 variants)
  • HEMOGLOBIN_A(2)_ADRIA (1 variants)
  • HEMOGLOBIN_A(2)_TROODOS (1 variants)
  • HEMOGLOBIN_NYU (1 variants)
  • HEMOGLOBIN_A(2)_CORFU (1 variants)
  • HEMOGLOBIN_A(2)_NYU (1 variants)
  • HEMOGLOBIN_A(2)_FITZROY (1 variants)
  • HEMOGLOBIN_A(2)_CAPRI (1 variants)
  • HEMOGLOBIN_A(2)-PRIME (1 variants)
  • HEMOGLOBIN_A(2)_METAPONTO (1 variants)
  • HEMOGLOBIN_A(2)_MANZANARES (1 variants)
  • HEMOGLOBIN_FLATBUSH_(GEORGIA) (1 variants)
  • HEMOGLOBIN_A(2)_CANADA (1 variants)
  • HEMOGLOBIN_A(2)_SANT'_ANTIOCO (1 variants)
  • HEMOGLOBIN_A(2)_MELBOURNE (1 variants)
  • HEMOGLOBIN_A(2)_LUCANIA (1 variants)
  • HEMOGLOBIN_A(2)_MONREALE (1 variants)
  • HEMOGLOBIN_B(2) (1 variants)
  • HEMOGLOBIN_A(2)_WRENS (1 variants)
  • HEMOGLOBIN_A(2)_VICTORIA (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. These statistics are base on transcript: NM_000000519.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
1
clinvar
1
clinvar
 6
missense
3
clinvar
47
clinvar
 50
nonsense
1
clinvar
 1
start loss
0
frameshift
2
clinvar
 2
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 7 0 51 1 1

Highest pathogenic variant AF is 0.0000433684

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
HBDprotein_codingprotein_codingENST00000380299 32693
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.00001920.1561257160211257370.0000835
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.019974.41.330.00000365956
Missense in Polyphen3021.8241.3746336
Synonymous-0.8843629.91.210.00000142299
Loss of Function-0.96663.931.531.69e-749

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006150.0000615
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.0001140.000114
Middle Eastern0.0001090.000109
South Asian0.0001630.000163
Other0.000.00

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

pHI
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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