HBG2
hemoglobin subunit gamma 2, the group of Hemoglobin subunits
Basic information
Region (hg38): 11:5253188-5505605
Links
Phenotypes
GenCC
Source:
- hereditary persistence of fetal hemoglobin-beta-thalassemia syndrome (Supportive), mode of inheritance: AD
- hereditary persistence of fetal hemoglobin-sickle cell disease syndrome (Supportive), mode of inheritance: AR
- hemoglobinopathy Toms River (Supportive), mode of inheritance: AD
- cyanosis, transient neonatal (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Cyanosis, transient neonatal | AD | Hematologic | Though a range of severity has been described, some individuals have been reported as requiring supplemental oxygen and/or RBC transfusions | Hematologic | 6158500; 6174163; 6205403; 6208955; 2483933; 8811323; 12603090; 21561349; 22935660 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (15 variants)
- not_specified (8 variants)
- Cyanosis,_transient_neonatal (7 variants)
- HEMOGLOBIN_F_(MELBOURNE) (1 variants)
- HEMOGLOBIN_F_(SACROMONTE) (1 variants)
- HEMOGLOBIN_F_(HEATHER) (1 variants)
- HEMOGLOBIN_F_(GRANADA) (1 variants)
- HEMOGLOBIN_F_(SHANGHAI) (1 variants)
- HEMOGLOBIN_F_(KINGSTON) (1 variants)
- HEMOGLOBIN_F_(MARIETTA) (1 variants)
- HEMOGLOBIN_F_(PORT_ROYAL) (1 variants)
- HEMOGLOBIN_F_(BROOKLYN) (1 variants)
- HEMOGLOBIN_F_(ONODA) (1 variants)
- HEMOGLOBIN_F_(COSENZA) (1 variants)
- HEMOGLOBIN_F_(CARLTON) (1 variants)
- HEMOGLOBIN_F_(MALTA) (1 variants)
- HEMOGLOBIN_F_(OULED_RABAH) (1 variants)
- HEMOGLOBIN_F_(LODZ) (1 variants)
- HEMOGLOBIN_F_(CATALONIA) (1 variants)
- HEMOGLOBIN_F_(AUSTELL) (1 variants)
- HEMOGLOBIN_F_(CALTECH) (1 variants)
- HEMOGLOBIN_F_(KENNESTONE) (1 variants)
- HEMOGLOBIN_F_(VELETA) (1 variants)
- HEMOGLOBIN_F_(LA_GRANGE) (1 variants)
- HEMOGLOBIN_F_(MALAYSIA) (1 variants)
- HEMOGLOBIN_F_(POOLE) (1 variants)
- HEMOGLOBIN_F_(OAKLAND) (1 variants)
- HEMOGLOBIN_F_(CLARKE) (1 variants)
- HEMOGLOBIN_F_(WAYNESBORO) (1 variants)
- HEMOGLOBIN_F_(ALBAICIN) (1 variants)
- HEMOGLOBIN_F_(MINOO) (1 variants)
- HEMOGLOBIN_F_(AUCKLAND) (1 variants)
- HEMOGLOBIN_F_(LESVOS) (1 variants)
- HEMOGLOBIN_F_(FUCHU) (1 variants)
- HEMOGLOBIN_F_(CLAMART) (1 variants)
- HEMOGLOBIN_F_(TOKYO) (1 variants)
- HEMOGLOBIN_F_(EMIRATES) (1 variants)
- HEMOGLOBIN_F_(CALABRIA) (1 variants)
- HEMOGLOBIN_F_(MACEDONIA_II) (1 variants)
- HEMOGLOBIN_F_(URUMQI) (1 variants)
- HEMOGLOBIN_F_(COLUMBUS-GA) (1 variants)
- HEMOGLOBIN_F_(MEINOHAMA) (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HBG2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000184.3. 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 | 1 | |||||
| missense | 47 | 59 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 4 | 2 | 47 | 6 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HBG2 | protein_coding | protein_coding | ENST00000380259 | 3 | 392600 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.670 | 0.311 | 124730 | 0 | 1 | 124731 | 0.00000401 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.35 | 35 | 65.8 | 0.532 | 0.00000303 | 930 |
| Missense in Polyphen | 3 | 22.137 | 0.13552 | 348 | ||
| Synonymous | 0.905 | 21 | 27.0 | 0.778 | 0.00000134 | 280 |
| Loss of Function | 1.76 | 0 | 3.61 | 0.00 | 1.53e-7 | 49 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000995 | 0.0000995 |
| 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.;
- Disease
- DISEASE: Cyanosis transient neonatal (TNCY) [MIM:613977]: A disorder characterized by cyanosis in the fetus and neonate, due to a defect in the fetal hemoglobin chain which has reduced affinity for oxygen. Some patients develop anemia resulting from increased destruction of red cells containing abnormal or unstable hemoglobin. The cyanosis resolves spontaneously by 5 to 6 months of age or earlier, as the adult beta-globin chain is produced and replaces the fetal gamma-globin chain. {ECO:0000269|PubMed:19065339, ECO:0000269|PubMed:21561349, ECO:0000269|PubMed:24502349, ECO:0000269|PubMed:2470017, ECO:0000269|PubMed:2483933, ECO:0000269|PubMed:7741137}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- ATF-2 transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.0956
Intolerance Scores
- loftool
- 0.188
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.443
- hipred
- N
- hipred_score
- 0.238
- ghis
- 0.472
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.101
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;organic acid binding;metal ion binding