ABCB6
ATP binding cassette subfamily B member 6 (Langereis blood group), the group of ATP binding cassette subfamily B|Blood group antigens
Basic information
Region (hg38): 2:219209772-219218994
Links
Phenotypes
GenCC
Source:
- microphthalmia, isolated, with coloboma 7 (Limited), mode of inheritance: AD
- microphthalmia, isolated, with coloboma 7 (Limited), mode of inheritance: AD
- dyschromatosis universalis hereditaria (Supportive), mode of inheritance: AD
- familial pseudohyperkalemia (Supportive), mode of inheritance: AD
- microphthalmia, isolated, with coloboma (Supportive), mode of inheritance: AD
- dyschromatosis universalis hereditaria 3 (Limited), mode of inheritance: AD
- microphthalmia, isolated, with coloboma 7 (Limited), mode of inheritance: AD
- dyschromatosis universalis hereditaria 3 (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Pseudohyperkalemia, familial, 2, due to red cell leak; Blood group, Langereis system | AD/BG | Hematologic | Variants related to Familial pseudohyperkalemia may be important related to transfusion management; Variants associated with a blood group may be important in specific situations (eg, related to transfusion) | Dermatologic; Hematologic; Ophthalmologic | 5790273; 22246506; 22226084; 23180570; 23519333; 24947683 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (138 variants)
- Inborn_genetic_diseases (93 variants)
- ABCB6-related_disorder (19 variants)
- Microphthalmia,_isolated,_with_coloboma_7 (15 variants)
- Dyschromatosis_universalis_hereditaria_3 (15 variants)
- Langereis_blood_group (13 variants)
- Acute_intermittent_porphyria (9 variants)
- Familial_pseudohyperkalemia (8 variants)
- Protoporphyria,_erythropoietic,_1 (8 variants)
- Variegate_porphyria (6 variants)
- Hereditary_coproporphyria (5 variants)
- not_specified (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCB6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005689.4. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 19 | 20 | ||||
| missense | 156 | 14 | 183 | |||
| nonsense | 6 | |||||
| start loss | 0 | |||||
| frameshift | 10 | 13 | ||||
| splice donor/acceptor (+/-2bp) | 5 | |||||
| Total | 5 | 4 | 175 | 36 | 7 |
Highest pathogenic variant AF is 0.0000247839
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ABCB6 | protein_coding | protein_coding | ENST00000265316 | 19 | 9223 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 8.60e-19 | 0.347 | 125411 | 0 | 337 | 125748 | 0.00134 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.139 | 507 | 498 | 1.02 | 0.0000299 | 5354 |
| Missense in Polyphen | 189 | 184.3 | 1.0255 | 2008 | ||
| Synonymous | -1.55 | 234 | 206 | 1.14 | 0.0000125 | 1788 |
| Loss of Function | 1.68 | 35 | 47.5 | 0.737 | 0.00000264 | 455 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00504 | 0.00500 |
| Ashkenazi Jewish | 0.000101 | 0.0000992 |
| East Asian | 0.00191 | 0.00190 |
| Finnish | 0.00126 | 0.00125 |
| European (Non-Finnish) | 0.00102 | 0.000932 |
| Middle Eastern | 0.00191 | 0.00190 |
| South Asian | 0.000803 | 0.000719 |
| Other | 0.00118 | 0.00114 |
dbNSFP
Source:
- Function
- FUNCTION: Binds heme and porphyrins and functions in their ATP- dependent uptake into the mitochondria. Plays a crucial role in heme synthesis. {ECO:0000269|PubMed:10837493, ECO:0000269|PubMed:17006453}.;
- Disease
- DISEASE: Microphthalmia, isolated, with coloboma, 7 (MCOPCB7) [MIM:614497]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. Ocular colobomas are a set of malformations resulting from abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure (optic fissure). {ECO:0000269|PubMed:22226084}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Dyschromatosis universalis hereditaria 3 (DUH3) [MIM:615402]: An autosomal dominant pigmentary genodermatosis characterized by a mixture of hyperpigmented and hypopigmented macules distributed randomly over the body, that appear in infancy or early childhood. The trunk and extremities are the dominant sites of abnormal pigmentation. Facial lesions can be seen in 50% of affected individuals, but involvement of palms and soles is unusual. Abnormalities of hair and nails have also been reported. Dyschromatosis universalis hereditaria may be associated with abnormalities of dermal connective tissue, nerve tissue, or other systemic complications. {ECO:0000269|PubMed:23519333, ECO:0000269|PubMed:24224009, ECO:0000269|PubMed:24498303, ECO:0000269|PubMed:25288164}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Pseudohyperkalemia, familial, 2, due to red cell leak (PSHK2) [MIM:609153]: A dominantly inherited condition characterized by increased serum potassium levels, measured in whole-blood specimens stored at or below room temperature. This condition is not accompanied by clinical symptoms or biological signs except for borderline abnormalities of red cell shape. {ECO:0000269|PubMed:23180570, ECO:0000269|PubMed:24947683}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- ABC transporters - Homo sapiens (human);Transport of small molecules;ABC-family proteins mediated transport;Mitochondrial ABC transporters
(Consensus)
Intolerance Scores
- loftool
- 0.165
- rvis_EVS
- -0.37
- rvis_percentile_EVS
- 28.26
Haploinsufficiency Scores
- pHI
- 0.124
- hipred
- N
- hipred_score
- 0.251
- ghis
- 0.602
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.558
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Abcb6
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cellular phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- abcb6a
- Affected structure
- pupil
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- porphyrin-containing compound biosynthetic process;cellular iron ion homeostasis;brain development;heme transport;skin development;transmembrane transport
- Cellular component
- Golgi membrane;nucleoplasm;mitochondrion;mitochondrial envelope;mitochondrial outer membrane;endosome;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;cytosol;plasma membrane;endosome membrane;integral component of mitochondrial outer membrane;ATP-binding cassette (ABC) transporter complex;extracellular exosome
- Molecular function
- ATP binding;heme transporter activity;heme-transporting ATPase activity;efflux transmembrane transporter activity;heme binding