ABCA13

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

Basic information

Region (hg38): 7:48171458-48647497

Links

ENSG00000179869 ∙ NCBI:154664 ∙ OMIM:607807 ∙ HGNC:14638 ∙ Uniprot:Q86UQ4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCA13 gene.

• not_specified (692 variants)
• not_provided (94 variants)
• ABCA13-related_disorder (21 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (2 variants)
• ABCA13-related_neurodevelopmental_condition (2 variants)
• Intellectual_disability_without_epilepsy (2 variants)
• Schizophrenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCA13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152701.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				22	6	28
missense			624	89	27	740
nonsense		1	2			3
start loss						0
frameshift	1	1	5			7
splice donor/acceptor (+/-2bp)		1	2	2		5
Total	1	3	633	113	33

Highest pathogenic variant AF is 0.0000682064

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCA13	protein_coding	protein_coding	ENST00000435803	62	476038

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.78e-114	6.09e-15	123077	10	1585	124672	0.00642

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.52	2662	2.45e+3	1.09	0.000124	33330
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00888	0.00879
Ashkenazi Jewish	0.00815	0.00818
East Asian	0.0230	0.0221
Finnish	0.00838	0.00830
European (Non-Finnish)	0.00435	0.00425
Middle Eastern	0.0230	0.0221
South Asian	0.00849	0.00774
Other	0.00640	0.00613

dbNSFP

Source: dbNSFP

• Pathway: ABC transporters - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0733

Intolerance Scores

• loftool: 0.0414
• rvis_EVS: 4.73
• rvis_percentile_EVS: 99.79

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0688

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abca13
• Phenotype: homeostasis/metabolism phenotype; reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: lipid transport;neutrophil degranulation;transmembrane transport
• Cellular component: plasma membrane;integral component of membrane;secretory granule membrane;azurophil granule membrane;intracellular membrane-bounded organelle
• Molecular function: lipid transporter activity;ATP binding;ATPase activity, coupled to transmembrane movement of substances