ABCA13

protein-coding

ATP binding cassette subfamily A member 13, the group of ATP binding cassette subfamily A

Gene summary

In human, the ATP-binding cassette (ABC) family of transmembrane transporters has at least 48 genes and 7 gene subfamilies. This gene is a member of ABC gene subfamily A (ABCA). Genes within the ABCA family typically encode several thousand amino acids. Like other ABC transmembrane transporter proteins, this protein has 12 or more transmembrane alpha-helix domains that likely arrange to form a single central chamber with multiple substrate binding sites. It is also predicted to have two large extracellular domains and two nucleotide binding domains as is typical for ABCA proteins. Alternative splice variants have been described but their biological validity has not been demonstrated.[provided by RefSeq, Mar 2009]

MANE transcript

NM_152701.5

Inheritance

—

ClinVar variants

P:4U:771B:154

Top phenotype

ABCA13-related disorder

gnomAD constraint

pLI —, LoF o/e 0.92

Max pathogenic AF

—

Genomic locus

chr7:48,171,458-48,647,497

External References & Databases

Ensembl (ENSG00000179869)

Transcript & Mutation Effects

hg38 • Region Span ~476.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

schizophreniaLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0005090

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ABCA13 variants in ClinVar

10 Conditions Cataloged

not specifiedTotal: 788

not providedTotal: 105

ABCA13-related disorderTotal: 33

EBV-positive nodal T- and NK-cell lymphomaTotal: 2

ABCA13-related neurodevelopmental conditionTotal: 2

Intellectual disability without epilepsyTotal: 2

AutismTotal: 1

Neuropsychiatric disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152701.5. 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			4 clinvar	24 clinvar	6 clinvar	34
missense			740 clinvar	97 clinvar	25 clinvar	862
nonsense		1 clinvar	11 clinvar			12
start loss						0
frameshift	1 clinvar	1 clinvar	8 clinvar			10
splice donor/acceptor (+/-2bp)		1 clinvar	8 clinvar	2 clinvar		11
Total	1	3	771	123	31	929

Highest pathogenic variant AF is 0.0000682064

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152701.5	RefSeq	NP_689914.3	62	MANE Select
ENST00000435803.6	Ensembl	ENSP00000411096.1	62	MANE Select
ENST00000411975.5	Ensembl	ENSP00000391042.1	19	Standard
ENST00000417403.5	Ensembl	ENSP00000409268.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

ABC transporters - Homo sapiens (human)
Neutrophil degranulation
Innate Immune System
Immune System

Biological Process

lipid transport
neutrophil degranulation
transmembrane transport

Molecular Function

lipid transporter activity
ATP binding
ATPase activity, coupled to transmembrane movement of substances

Cellular Component

plasma membrane
integral component of membrane
secretory granule membrane
azurophil granule membrane
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000435803
Coding exons: 62
Length: 476038
Individuals with no LoFs: 123077
Homozygous LoFs: 10
Heterozygous LoFs: 1585
Defined: 124672
p: 0.00642

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.52	2662	2.45e+3	1.09	0.000124	33330
Missense (PolyPhen)		602	584.33	1.0302		8110
Synonymous	-0.998	987	948	1.04	0.0000508	9484
Loss of Function	1.11	183	200	0.915	0.00000969	2687

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0060	0.0059	notable
Latino/Admixed American	0.0029	0.0028	notable
Ashkenazi Jewish	0.0082	0.0082	notable
East Asian	0.023	0.022	notable
Finnish	0.0084	0.0083	notable
European (Non-Finnish)	0.0044	0.0043	notable
South Asian	0.0085	0.0077	notable
Other	0.0064	0.0061	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0733

Intolerance Scores

LoFtool: 0.0414
RVIS EVS: 4.73
RVIS percentile EVS: 99.79

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0688

Gene Damage Prediction

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