ABCB7

ATP binding cassette subfamily B member 7, the group of ATP binding cassette subfamily B

Basic information

Region (hg38): X:75051047-75156732

Previous symbols: [ "ABC7" ]

Links

ENSG00000131269 ∙ NCBI:22 ∙ OMIM:300135 ∙ HGNC:48 ∙ Uniprot:O75027 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• X-linked sideroblastic anemia with ataxia (Moderate), mode of inheritance: XL
• X-linked sideroblastic anemia with ataxia (Definitive), mode of inheritance: XLR
• X-linked sideroblastic anemia with ataxia (Strong), mode of inheritance: XL
• X-linked sideroblastic anemia with ataxia (Strong), mode of inheritance: XLR
• X-linked sideroblastic anemia with ataxia (Supportive), mode of inheritance: XL
• X-linked sideroblastic anemia with ataxia (Strong), mode of inheritance: XL
• X-linked sideroblastic anemia with ataxia (Definitive), mode of inheritance: XL
• mitochondrial disease (Moderate), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Anemia, sideroblastic, and spinocerebellar ataxia	XL	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; Neurologic	4045952; 10196363; 20301496; 22398176

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCB7 gene.

• not provided (134 variants)
• X-linked sideroblastic anemia with ataxia (23 variants)
• not specified (17 variants)
• Sideroblastic Anemia and Ataxia (8 variants)
• Inborn genetic diseases (8 variants)
• ABCB7-related condition (2 variants)
• Spinocerebellar ataxia, X-linked (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCB7 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			4	25	6	35
missense	1	4	31	9	10	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			7	6	2	15
non coding			2	27	22	51
Total	1	4	37	61	38

Highest pathogenic variant AF is 0.0000358

Variants in ABCB7

This is a list of pathogenic ClinVar variants found in the ABCB7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-75053250-AATCTT-A			Likely benign (Mar 01, 2023)
X-75053257-T-C		X-linked sideroblastic anemia with ataxia	Uncertain significance (Jan 13, 2018)
X-75053373-G-A			Likely benign (Dec 05, 2023)
X-75053419-T-C		Inborn genetic diseases	Uncertain significance (Mar 07, 2024)
X-75053425-T-G			Uncertain significance (Dec 06, 2023)
X-75053428-T-G			Uncertain significance (Oct 01, 2023)
X-75053477-G-T			Benign (Nov 28, 2023)
X-75053497-C-T		ABCB7-related disorder	Uncertain significance (Jun 05, 2023)
X-75053508-T-C			Likely benign (Nov 07, 2022)
X-75053556-A-G		X-linked sideroblastic anemia with ataxia	Uncertain significance (Jan 13, 2018)
X-75053563-G-A		X-linked sideroblastic anemia with ataxia	Uncertain significance (Jan 13, 2020)
X-75053566-C-T		Inborn genetic diseases	Uncertain significance (Mar 31, 2022)
X-75053569-C-T			Uncertain significance (Apr 03, 2023)
X-75053574-G-A			Likely benign (Jan 29, 2024)
X-75053585-C-T		Spinocerebellar ataxia, X-linked • Inborn genetic diseases	Likely pathogenic (Jan 15, 2016)
X-75053593-G-A			Likely benign (Aug 31, 2023)
X-75053602-T-G			Likely benign (May 15, 2023)
X-75053609-C-T			Likely benign (Jul 07, 2018)
X-75053619-G-A			Likely benign (Feb 25, 2020)
X-75053854-G-C			Likely benign (Aug 03, 2018)
X-75060009-T-C			Benign (Jul 31, 2018)
X-75060016-TATA-T			Benign (Jul 31, 2018)
X-75060206-A-T		not specified	Benign (Jan 29, 2024)
X-75060244-A-G			Likely benign (Mar 03, 2023)
X-75060298-T-C			Uncertain significance (May 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCB7	protein_coding	protein_coding	ENST00000253577	16	103453

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000619	122732	702	1208	124642	0.00769

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.90	145	282	0.514	0.0000199	4888
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0115	0.0110
Ashkenazi Jewish	0.0111	0.00831
East Asian	0.0000724	0.0000546
Finnish	0.00352	0.00261
European (Non-Finnish)	0.0169	0.0122
Middle Eastern	0.0000724	0.0000546
South Asian	0.00355	0.00222
Other	0.0124	0.00923

dbNSFP

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.
• Pathway: ABC transporters - Homo sapiens (human);Transport of small molecules;ABC-family proteins mediated transport;Mitochondrial ABC transporters (Consensus)

Recessive Scores

• pRec: 0.517

Intolerance Scores

• loftool: 0.0561
• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.69

Haploinsufficiency Scores

• pHI: 0.417
• hipred: Y
• hipred_score: 0.628
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.169

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Abcb7
• Phenotype: embryo phenotype; liver/biliary system 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: cellular iron ion homeostasis;heme transport;transmembrane transport
• Cellular component: mitochondrial inner membrane;integral component of membrane
• Molecular function: ATP binding;heme transporter activity;ATPase activity, coupled to transmembrane movement of substances