ABCB5

ATP binding cassette subfamily B member 5, the group of ATP binding cassette subfamily B

Basic information

Region (hg38): 7:20615666-20777038

Links

ENSG00000004846 ∙ NCBI:340273 ∙ OMIM:611785 ∙ HGNC:46 ∙ Uniprot:Q2M3G0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCB5 gene.

• Inborn genetic diseases (52 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCB5 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				3		3
missense			51	3	3	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	51	6	4

Variants in ABCB5

This is a list of pathogenic ClinVar variants found in the ABCB5 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-20623329-A-G		not specified	Uncertain significance (Aug 08, 2022)
7-20626567-G-C		not specified	Uncertain significance (Jan 25, 2023)
7-20626583-G-T		not specified	Uncertain significance (Jan 22, 2024)
7-20628718-C-A		not specified	Uncertain significance (Jan 31, 2023)
7-20628726-C-G		not specified	Uncertain significance (May 05, 2023)
7-20628748-G-A		not specified	Uncertain significance (Jun 28, 2022)
7-20628755-G-A		not specified	Uncertain significance (May 31, 2022)
7-20628758-C-A		not specified	Uncertain significance (Oct 03, 2022)
7-20628820-C-G		not specified	Uncertain significance (Aug 16, 2021)
7-20628830-C-T		not specified	Uncertain significance (Sep 12, 2023)
7-20632071-A-G		not specified	Uncertain significance (Oct 24, 2023)
7-20643234-A-T		not specified	Uncertain significance (Jan 04, 2022)
7-20643245-T-C		not specified	Uncertain significance (May 11, 2022)
7-20643251-T-C		not specified	Uncertain significance (Nov 08, 2021)
7-20643365-C-T		not specified	Uncertain significance (Nov 10, 2022)
7-20643499-T-C		not specified	Uncertain significance (Jan 17, 2024)
7-20643541-T-C		not specified	Uncertain significance (Dec 21, 2023)
7-20643546-G-A		not specified	Likely benign (Sep 29, 2023)
7-20643559-A-G		not specified	Uncertain significance (Sep 16, 2021)
7-20643607-T-A		not specified	Uncertain significance (Mar 20, 2023)
7-20643631-G-T		not specified	Uncertain significance (Sep 19, 2022)
7-20645746-T-G			Benign (Jun 12, 2018)
7-20645774-A-C		not specified	Uncertain significance (Feb 03, 2022)
7-20646002-A-C		not specified	Uncertain significance (May 03, 2023)
7-20647550-A-T		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCB5	protein_coding	protein_coding	ENST00000404938	27	161829

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.51e-37	0.0000482	106790	3319	15639	125748	0.0785

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.98	814	670	1.22	0.0000350	8173
Missense in Polyphen		282	233.18	1.2093		2815
Synonymous	-2.13	279	237	1.18	0.0000131	2420
Loss of Function	0.683	60	66.0	0.909	0.00000391	797

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.286	0.282
Ashkenazi Jewish	0.0261	0.0247
East Asian	0.497	0.432
Finnish	0.0870	0.0832
European (Non-Finnish)	0.00808	0.00756
Middle Eastern	0.497	0.432
South Asian	0.0890	0.0791
Other	0.0620	0.0561

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Drug efflux transporter present in a number of stem cells that acts as a regulator of cellular differentiation. Able to mediate efflux from cells of the rhodamine dye and of the therapeutic drug doxorubicin. Specifically present in limbal stem cells, where it plays a key role in corneal development and repair. {ECO:0000269|PubMed:12960149, ECO:0000269|PubMed:15205344, ECO:0000269|PubMed:15899824, ECO:0000269|PubMed:22306008}.
• Pathway: ABC transporters - Homo sapiens (human);Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Recessive Scores

• pRec: 0.0931

Intolerance Scores

• loftool: 0.0314
• rvis_EVS: 4.18
• rvis_percentile_EVS: 99.7

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.241

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.130

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Abcb5
• Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); pigmentation phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: drug transmembrane transport;cell differentiation;regulation of membrane potential;xenobiotic transport;compound eye corneal lens development;transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: ATP binding;xenobiotic transmembrane transporting ATPase activity;efflux transmembrane transporter activity