APBA2

amyloid beta precursor protein binding family A member 2, the group of PDZ domain containing

Basic information

Region (hg38): 15:28884482-29118315

Previous symbols: [ "X11L", "MINT2" ]

Links

ENSG00000034053 ∙ NCBI:321 ∙ OMIM:602712 ∙ HGNC:579 ∙ Uniprot:Q99767 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• epilepsy (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the APBA2 gene.

• not provided (27 variants)
• Inborn genetic diseases (25 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APBA2 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				9	9	18
missense			27	2	2	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					2	2
Total	0	0	27	11	13

Variants in APBA2

This is a list of pathogenic ClinVar variants found in the APBA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-29053916-G-A		not specified	Uncertain significance (Aug 02, 2022)
15-29053917-C-T		APBA2-related disorder	Benign (Dec 31, 2019)
15-29053918-G-A			Likely benign (Dec 27, 2017)
15-29053989-G-C		not specified	Uncertain significance (Oct 12, 2021)
15-29054039-G-A		APBA2-related disorder	Benign (Feb 26, 2019)
15-29054048-G-A		APBA2-related disorder	Benign/Likely benign (May 01, 2022)
15-29054054-C-T		APBA2-related disorder	Likely benign (Mar 20, 2023)
15-29054060-A-G		not specified	Uncertain significance (Feb 15, 2023)
15-29054103-C-T		APBA2-related disorder	Likely benign (Apr 25, 2019)
15-29054113-G-A		not specified	Uncertain significance (May 31, 2023)
15-29054145-C-T		APBA2-related disorder	Benign (Dec 31, 2019)
15-29054184-C-T		APBA2-related disorder	Likely benign (May 03, 2019)
15-29054187-C-T		APBA2-related disorder	Benign/Likely benign (Apr 01, 2019)
15-29054235-C-T			Likely benign (Oct 23, 2018)
15-29054241-G-A			Likely benign (Apr 03, 2018)
15-29054265-C-T		APBA2-related disorder	Benign (Dec 31, 2019)
15-29054310-G-A		APBA2-related disorder	Likely benign (Feb 20, 2019)
15-29054315-C-T		APBA2-related disorder	Benign (Dec 31, 2019)
15-29054320-G-A		not specified	Uncertain significance (Sep 17, 2021)
15-29054324-C-T		not specified	Uncertain significance (Dec 16, 2021)
15-29054326-C-T		not specified	Uncertain significance (Feb 12, 2024)
15-29054329-C-T		not specified	Uncertain significance (Feb 27, 2023)
15-29054370-C-T		APBA2-related disorder	Likely benign (Oct 29, 2019)
15-29054387-C-T		APBA2-related disorder	Benign (Dec 31, 2019)
15-29054403-C-T		APBA2-related disorder	Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APBA2	protein_coding	protein_coding	ENST00000558402	12	280890

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.743	0.257	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	363	450	0.806	0.0000301	4958
Missense in Polyphen		71	125.4	0.5662		1350
Synonymous	-1.53	223	196	1.14	0.0000158	1419
Loss of Function	4.15	6	30.8	0.195	0.00000145	366

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative function in synaptic vesicle exocytosis by binding to STXBP1, an essential component of the synaptic vesicle exocytotic machinery. May modulate processing of the amyloid-beta precursor protein (APP) and hence formation of APP-beta.
• Pathway: Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.205

Intolerance Scores

• loftool: 0.451
• rvis_EVS: -1.39
• rvis_percentile_EVS: 4.31

Haploinsufficiency Scores

• pHI: 0.255
• hipred: Y
• hipred_score: 0.733
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.804

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apba2
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: in utero embryonic development;chemical synaptic transmission;nervous system development;locomotory behavior;regulation of gene expression;protein transport;multicellular organism growth;regulation of synaptic vesicle exocytosis
• Cellular component: cytoplasm;plasma membrane;synaptic vesicle;dendritic spine;synapse;Schaffer collateral - CA1 synapse
• Molecular function: amyloid-beta binding;protein binding