ABCB9

protein-coding

ATP binding cassette subfamily B member 9, 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 family member functions in the translocation of peptides from the cytosol into the lysosomal lumen. Alternative splicing of this gene results in distinct isoforms which are likely to have different substrate specificities. [provided by RefSeq, Jul 2011]

MANE transcript

NM_019625.4

Inheritance

—

ClinVar variants

U:148B:18

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr12:122,920,951-122,981,649

External References & Databases

Ensembl (ENSG00000150967)

Transcript & Mutation Effects

hg38 • Region Span ~60.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ABCB9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 153

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_019625.4. 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			2 clinvar	12 clinvar		14
missense			139 clinvar	6 clinvar		145
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	148	18	0	166

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_019625.4	RefSeq	NP_062571.1	11	MANE Select
ENST00000280560.13	Ensembl	ENSP00000280560.8	11	MANE Select
NM_001243013.2	RefSeq	NP_001229942.1	10	Standard
NM_001243014.2	RefSeq	NP_001229943.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Lysosome - Homo sapiens (human)
ABC transporters - Homo sapiens (human)
Transport of small molecules
ABC-family proteins mediated transport

Biological Process

antigen processing and presentation of peptide antigen via MHC class I
protein transport
peptide transport
oligopeptide transmembrane transport
transmembrane transport

Molecular Function

protein binding
ATP binding
oligopeptide-transporting ATPase activity
peptide-transporting ATPase activity
transmembrane transporter activity

Cellular Component

lysosome
lysosomal membrane
early endosome
endoplasmic reticulum
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000542678
Coding exons: 11
Length: 60699
Individuals with no LoFs: 125712
Homozygous LoFs: 0
Heterozygous LoFs: 36
Defined: 125748
p: 0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.01	432	495	0.872	0.0000340	4925
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00032	0.00032	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00027	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.133

Intolerance Scores

LoFtool: 0.0299
RVIS EVS: -1.82
RVIS percentile EVS: 2.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.275

Gene Damage Prediction

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