ABCB9

ATP binding cassette subfamily B member 9, the group of ATP binding cassette subfamily B

Basic information

Region (hg38): 12:122920950-122981649

Links

ENSG00000150967 ∙ NCBI:23457 ∙ OMIM:605453 ∙ HGNC:50 ∙ Uniprot:Q9NP78 ∙ 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 ABCB9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCB9 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				2		2
missense			49	4		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			51	2		53
Total	0	0	100	8	0

Variants in ABCB9

This is a list of pathogenic ClinVar variants found in the ABCB9 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-122929934-C-T		not specified	Uncertain significance (Feb 28, 2024)
12-122929993-C-T		not specified	Uncertain significance (Mar 06, 2023)
12-122930060-C-T		not specified	Uncertain significance (Jun 03, 2024)
12-122930062-C-T		not specified	Uncertain significance (Dec 09, 2023)
12-122930078-C-A		not specified	Uncertain significance (Dec 16, 2022)
12-122930091-C-T		not specified	Likely benign (Aug 22, 2023)
12-122930093-C-T		not specified	Uncertain significance (Dec 27, 2023)
12-122930118-C-T		not specified	Likely benign (May 15, 2024)
12-122930119-G-A		not specified	Uncertain significance (Oct 05, 2023)
12-122930133-C-T		not specified	Likely benign (Jun 02, 2023)
12-122932206-C-T		not specified	Uncertain significance (Nov 06, 2023)
12-122932257-G-A		not specified	Uncertain significance (Jul 26, 2022)
12-122935308-C-T		not specified	Uncertain significance (Jul 06, 2021)
12-122935337-A-G		not specified	Uncertain significance (May 17, 2023)
12-122935389-T-C		not specified	Uncertain significance (Apr 01, 2024)
12-122935395-G-A		not specified	Uncertain significance (Nov 13, 2023)
12-122935407-C-A		not specified	Uncertain significance (Mar 02, 2023)
12-122940134-C-T		not specified	Uncertain significance (Apr 15, 2024)
12-122940146-T-C		not specified	Uncertain significance (May 04, 2023)
12-122940169-C-T		not specified	Uncertain significance (Jun 30, 2023)
12-122940172-C-T		not specified	Uncertain significance (Dec 06, 2022)
12-122940194-T-A		not specified	Uncertain significance (Feb 17, 2022)
12-122940260-C-T		not specified	Uncertain significance (Feb 23, 2023)
12-122940265-G-C		not specified	Likely benign (Sep 22, 2023)
12-122940836-G-A		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCB9	protein_coding	protein_coding	ENST00000542678	11	60699

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000252	0.999	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	432	495	0.872	0.0000340	4925
Missense in Polyphen		145	168.12	0.86247		1656
Synonymous	0.486	218	227	0.959	0.0000170	1626
Loss of Function	2.96	11	27.9	0.394	0.00000127	314

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000321	0.000321
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.000267	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ATP-dependent low-affinity peptide transporter which translocates a broad spectrum of peptides from the cytosol to the lysosomal lumen. Displays a broad peptide length specificity from 6-mer up to at least 59-mer peptides with an optimum of 23-mers. Favors positively charged, aromatic or hydrophobic residues in the N- and C-terminal positions whereas negatively charged residues as well as asparagine and methionine are not favored. {ECO:0000269|PubMed:15863492, ECO:0000269|PubMed:17977821, ECO:0000269|PubMed:18434309}.
• Pathway: Lysosome - Homo sapiens (human);ABC transporters - Homo sapiens (human);Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.0299
• rvis_EVS: -1.82
• rvis_percentile_EVS: 2.16

Haploinsufficiency Scores

• pHI: 0.269
• hipred: N
• hipred_score: 0.393
• ghis: 0.676

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.275

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abcb9
• Phenotype: endocrine/exocrine gland phenotype

Gene ontology

• Biological process: antigen processing and presentation of peptide antigen via MHC class I;protein transport;peptide transport;oligopeptide transmembrane transport;transmembrane transport
• Cellular component: lysosome;lysosomal membrane;early endosome;endoplasmic reticulum;integral component of membrane;integral component of endoplasmic reticulum membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding;ATP binding;oligopeptide-transporting ATPase activity;peptide-transporting ATPase activity;transmembrane transporter activity;ATPase activity, coupled to transmembrane movement of substances;protein homodimerization activity