ABCB7

protein-coding

ATP 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]

Previous symbols:
  • ABC7

MANE transcript

NM_001271696.3

Inheritance

XL, XLR

ClinVar variants

P:11U:227B:104

Top phenotype

Spinocerebellar ataxia, x-linked 6, with or without sideroblastic anemia

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:75,051,048-75,156,732

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~105.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

X-linked sideroblastic anemia with ataxiaSTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0010524

Submitter: PanelApp Australia

X-linked sideroblastic anemia with ataxiaSUPPORTIVE

Inheritance Pattern: XL

Disease ID:MONDO:0010524

Submitter: Orphanet

X-linked sideroblastic anemia with ataxiaSTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0010524

Submitter: Labcorp Genetics (formerly Invitae)

X-linked sideroblastic anemia with ataxiaSTRONG

Inheritance Pattern: XLR

Disease ID:MONDO:0010524

Submitter: Labcorp Genetics (formerly Invitae)

X-linked sideroblastic anemia with ataxiaDEFINITIVE

Inheritance Pattern: XL

Disease ID:MONDO:0010524

Submitter: G2P

mitochondrial diseaseMODERATE

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).

X-linked sideroblastic anemia with ataxiaSTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0010524

Submitter: Genomics England PanelApp

X-linked sideroblastic anemia with ataxiaMODERATE

Inheritance Pattern: XL

Disease ID:MONDO:0010524

Submitter: Illumina

Clinical Genomic Database (CGD)

Spinocerebellar ataxia, x-linked 6, with or without sideroblastic anemiaXL

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

Refs: 4045952; 10196363; 20301496; 22398176Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ABCB7 variants in ClinVar

9 Conditions Cataloged
not providedTotal: 240
not specifiedTotal: 50
Inborn genetic diseasesTotal: 48
X-linked sideroblastic anemia with ataxiaTotal: 31
ABCB7-related disorderTotal: 19
Spinocerebellar ataxia, X-linkedTotal: 1
EpilepsyTotal: 1
Mitochondrial diseaseTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
21
clinvar
59
clinvar
12
clinvar
92
missense
4
clinvar
7
clinvar
175
clinvar
25
clinvar
7
clinvar
218
nonsense
4
clinvar
4
start loss
1
clinvar
1
frameshift
0
splice donor/acceptor (+/-2bp)
26
clinvar
1
clinvar
27
Total472278519342

Highest pathogenic variant AF is 0.00004236503

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001271696.3RefSeqNP_001258625.116MANE Select
ENST00000373394.8EnsemblENSP00000362492.316MANE Select
NM_001271697.3RefSeqNP_001258626.115Standard
NM_001271698.3RefSeqNP_001258627.115Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.901452820.5140.00001994888
Missense (PolyPhen)18109.180.164871975
Synonymous-0.09581051041.010.000007621507
Loss of Function4.86027.50.000.00000210461

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00200.0015notable
Latino/Admixed American0.00950.0076notable
Ashkenazi Jewish0.0110.0083notable
East Asian0.0000720.000055rare
Finnish0.00350.0026notable
European (Non-Finnish)0.0170.012notable
South Asian0.00360.0022notable
Other0.0120.0092notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.