HBG1
Basic information
Region (hg38): 11:5248269-5249857
Links
Phenotypes
GenCC
Source:
- 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:
| 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
- Hereditary_persistence_of_fetal_hemoglobin (8 variants)
- not_specified (7 variants)
- Fetal_hemoglobin_quantitative_trait_locus_1 (2 variants)
- not_provided (1 variants)
- HEMOGLOBIN_F_(JIANGSU) (1 variants)
- HEMOGLOBIN_F_(VICTORIA_JUBILEE) (1 variants)
- HEMOGLOBIN_F_(KOTOBUKI) (1 variants)
- HEMOGLOBIN_F_(BASKENT) (1 variants)
- HEMOGLOBIN_F_(IWATA) (1 variants)
- HEMOGLOBIN_F_(TEXAS_I) (1 variants)
- HEMOGLOBIN_F_(COBB) (1 variants)
- HEMOGLOBIN_F_(FOREST_PARK) (1 variants)
- HEMOGLOBIN_F_(WOODSTOCK) (1 variants)
- HEMOGLOBIN_F_(JAMAICA) (1 variants)
- HEMOGLOBIN_F_(BONAIRE) (1 variants)
- HEMOGLOBIN_F_(YAMAGUCHI) (1 variants)
- HEMOGLOBIN_F_(XIN-SU) (1 variants)
- HEMOGLOBIN_F_(DICKINSON) (1 variants)
- HEMOGLOBIN_F_(SIENA) (1 variants)
- HEMOGLOBIN_F_(KUALA_LUMPUR) (1 variants)
- HEMOGLOBIN_F_(CALLUNA) (1 variants)
- HEMOGLOBIN_F_(IZUMI) (1 variants)
- HEMOGLOBIN_F_(BEECH_ISLAND) (1 variants)
- HEMOGLOBIN_F_(PENDERGRASS) (1 variants)
- HEMOGLOBIN_F_(PORDENONE) (1 variants)
- HEMOGLOBIN_F_(HULL) (1 variants)
- HEMOGLOBIN_F_(MACEDONIA-I) (1 variants)
- HEMOGLOBIN_F_(DAMMAM) (1 variants)
- HEMOGLOBIN_F_(XINJIANG) (1 variants)
- HEMOGLOBIN_F_(FUKUYAMA) (1 variants)
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. These statistics are base on transcript: NM_000000559.3. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 29 | 37 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 29 | 7 | 1 |
GnomAD
Source:
| 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:
- 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_CRISPR2
- 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