ABCA13

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

Basic information

Region (hg38): 7:48171457-48647497

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.

• Inborn genetic diseases (210 variants)
• not provided (79 variants)
• not specified (3 variants)
• ABCA13-related condition (3 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.

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				14	10	24
missense			205	27	23	255
nonsense			1			1
start loss						0
frameshift	1		1			2
inframe indel						0
splice donor/acceptor (+/-2bp)		1	1			2
splice region			2		4	6
non coding				1		1
Total	1	1	208	42	33

Highest pathogenic variant AF is 0.0000132

Variants in ABCA13

This is a list of pathogenic ClinVar variants found in the ABCA13 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-48171493-G-A		not specified	Conflicting classifications of pathogenicity (Jan 10, 2023)
7-48171551-C-T		not specified	Uncertain significance (Jan 23, 2023)
7-48192960-T-A		not specified	Uncertain significance (Apr 28, 2023)
7-48192983-T-C			Benign/Likely benign (Oct 01, 2023)
7-48193020-G-A		not specified	Uncertain significance (Jul 19, 2022)
7-48198316-G-T		not specified	Uncertain significance (Nov 08, 2022)
7-48198330-G-T		not specified	Uncertain significance (Mar 07, 2024)
7-48198365-G-A		ABCA13-related disorder	Uncertain significance (Sep 11, 2023)
7-48219460-G-A		not specified	Uncertain significance (May 05, 2023)
7-48219491-G-A		not specified	Uncertain significance (Mar 23, 2022)
7-48227272-A-G		ABCA13-related disorder • not specified	Conflicting classifications of pathogenicity (Apr 28, 2022)
7-48227276-G-T		not specified	Uncertain significance (Nov 03, 2022)
7-48227286-G-A		not specified	Uncertain significance (Jul 13, 2021)
7-48227350-C-T			Uncertain significance (Aug 31, 2022)
7-48227379-G-A		not specified	Uncertain significance (Sep 01, 2021)
7-48227397-G-T		not specified	Uncertain significance (Feb 28, 2024)
7-48234065-A-G		not specified	Uncertain significance (Jan 22, 2024)
7-48234084-A-G		not specified	Uncertain significance (Jan 31, 2024)
7-48234137-G-A		not specified	Uncertain significance (Jun 18, 2021)
7-48239270-G-T			Likely benign (Mar 01, 2024)
7-48239300-G-T		not specified	Uncertain significance (Jul 25, 2023)
7-48239322-C-T		not specified	Likely benign (Jan 31, 2024)
7-48239328-G-A		not specified	Uncertain significance (Dec 03, 2021)
7-48239387-G-C		not specified	Uncertain significance (Sep 01, 2021)
7-48240867-G-T		not specified	Uncertain significance (Jul 14, 2022)

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