ABCB7
protein-codingATP binding cassette subfamily B member 7, the group of ATP binding cassette subfamily B
Gene summary
The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance as well as antigen presentation. This gene encodes a half-transporter involved in the transport of heme from the mitochondria to the cytosol. With iron/sulfur cluster precursors as its substrates, this protein may play a role in metal homeostasis. Mutations in this gene have been associated with mitochondrial iron accumulation and isodicentric (X)(q13) and sideroblastic anemia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2012]
- ABC7
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~105.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: XL
Disease ID:MONDO:0010524
Submitter: PanelApp Australia
Inheritance Pattern: XL
Disease ID:MONDO:0010524
Submitter: Orphanet
Inheritance Pattern: XL
Disease ID:MONDO:0010524
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: XLR
Disease ID:MONDO:0010524
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: XL
Disease ID:MONDO:0010524
Submitter: G2P
Inheritance Pattern: XL
Disease ID:MONDO:0044970
Submitter: ClinGen
The relationship between *ABCB7* and primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of September 28, 2023. *ABCB7* encodes ATP-binding cassette, subfamily B, member 7. This protein is involved in the transport of iron between mitochondria and the cytosol (transport of iron-sulfur (Fe-S) clusters from the lumen of mitochondria to the cytosol), and pathogenic variants result in mitochondrial iron accumulation (since iron cannot be transferred to cytosol) that then causes oxidative stress. Furthermore, impaired iron homeostasis disrupts the heme synthesis pathway as Fe-S cluster assembly is essential for heme production. *ABCB7* was first reported in relation to X-linked primary mitochondrial disease in 1999 (PMID: 10196363, although these individuals were from a family first reported in 1985, PMID: 4045952) with four males affected by developmental delay, ataxia, dysmetria, dysarthria, and anemia. While various names have been given to the constellation of features seen in those with *ABCB7*-related disease including with X-linked sideroblastic anemia with ataxia (XLSA/A), pathogenic variants in this gene cause a primary mitochondrial disease. Therefore, the *ABCB7* phenotype has been lumped into one disease entity according to the ClinGen Lumping and Splitting Framework. Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included six unique missense variants identified in six kindreds (PMIDs: 10196363, 11050011, 11843825, 22398176, 26242992, 34354969). There were several affected males across these six kindreds. Some female carriers had mild hematologic changes but no neurologic features. Affected males had ataxia (non-progressive, typically noted early in life), sideroblastic anemia (typically mild, sometimes absent), and variable growth impairment. Other features seen include developmental delay, dysmetria, dysarthria, tremor, variable reflexes (brisk, diminished), spasticity, nystagmus, ophthalmoplegia, intellectual disability (in one individual), schizophrenia (in one individual), and seizures (in one individual). Some individuals were noted to have cerebellar hypoplasia on brain imaging while this was normal in others. Muscle biopsies and metabolic screening labs were not routinely reported in these cases. This gene-disease association is also supported by its known biochemical function (PMID: 33340416), model organisms including a medaka fish (PMID: 19046159), mouse (PMID: 16467350), and *Caenorhabditis elegans* (PMID: 21464130). In summary, there is moderate evidence to support the relationship between *ABCB7* and primary mitochondrial disease. While more evidence is needed to establish this relationship definitively, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Gene Curation Expert Panel on September 28, 2023 (SOP Version 9).
Inheritance Pattern: XL
Disease ID:MONDO:0010524
Submitter: Genomics England PanelApp
Inheritance Pattern: XL
Disease ID:MONDO:0010524
Submitter: Illumina
Clinical Genomic Database (CGD)
Manifestation: Hematologic; Neurologic
Intervention: General
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ABCB7 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001271696.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 21 | 59 | 12 | 92 | ||
| missense | 4 | 7 | 175 | 25 | 7 | 218 |
| nonsense | 4 | 4 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 26 | 1 | 27 | |||
| Total | 4 | 7 | 227 | 85 | 19 | 342 |
Highest pathogenic variant AF is 0.00004236503
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001258625.1 | 16 | MANE Select | |
| Ensembl | ENSP00000362492.3 | 16 | MANE Select | |
| RefSeq | NP_001258626.1 | 15 | Standard | |
| RefSeq | NP_001258627.1 | 15 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- ABC transporters - Homo sapiens (human)
- Transport of small molecules
- ABC-family proteins mediated transport
- Mitochondrial ABC transporters
Biological Process
- cellular iron ion homeostasis
- heme transport
- transmembrane transport
Molecular Function
- ATP binding
- heme transporter activity
- ATPase activity, coupled to transmembrane movement of substances
Cellular Component
- mitochondrial inner membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000253577
- Coding exons
- 16
- Length
- 103453
- Individuals with no LoFs
- 122732
- Homozygous LoFs
- 702
- Heterozygous LoFs
- 1208
- Defined
- 124642
- p
- 0.00769
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.90 | 145 | 282 | 0.514 | 0.0000199 | 4888 |
| Missense (PolyPhen) | 18 | 109.18 | 0.16487 | 1975 | ||
| Synonymous | -0.0958 | 105 | 104 | 1.01 | 0.00000762 | 1507 |
| Loss of Function | 4.86 | 0 | 27.5 | 0.00 | 0.00000210 | 461 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0020 | 0.0015 | notable |
| Latino/Admixed American | 0.0095 | 0.0076 | notable |
| Ashkenazi Jewish | 0.011 | 0.0083 | notable |
| East Asian | 0.000072 | 0.000055 | rare |
| Finnish | 0.0035 | 0.0026 | notable |
| European (Non-Finnish) | 0.017 | 0.012 | notable |
| South Asian | 0.0036 | 0.0022 | notable |
| Other | 0.012 | 0.0092 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Could be involved in the transport of heme from the mitochondria to the cytosol. Plays a central role in the maturation of cytosolic iron-sulfur (Fe/S) cluster-containing proteins.;
- Disease
- DISEASE: Anemia, sideroblastic, spinocerebellar ataxia (ASAT) [MIM:301310]: A X-linked recessive disorder characterized by an infantile to early childhood onset of non-progressive cerebellar ataxia and mild anemia, with hypochromia and microcytosis. {ECO:0000269|PubMed:10196363, ECO:0000269|PubMed:11050011, ECO:0000269|PubMed:11843825, ECO:0000269|PubMed:22398176}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.517
Intolerance Scores
- LoFtool
- 0.0561
- RVIS EVS
- 0.86
- RVIS percentile EVS
- 88.69
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.169
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |