APBA1

amyloid beta precursor protein binding family A member 1, the group of PDZ domain containing

Basic information

Region (hg38): 9:69427532-69672371

Previous symbols: [ "MINT1" ]

Links

ENSG00000107282 ∙ NCBI:320 ∙ OMIM:602414 ∙ HGNC:578 ∙ Uniprot:Q02410 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the APBA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APBA1 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				1	1	2
missense			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	2	1

Variants in APBA1

This is a list of pathogenic ClinVar variants found in the APBA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-69431332-T-G		not specified	Uncertain significance (Jun 10, 2022)
9-69432549-T-C		not specified	Uncertain significance (Feb 22, 2023)
9-69432565-C-T		not specified	Uncertain significance (Mar 31, 2023)
9-69432592-C-T		not specified	Uncertain significance (Jan 03, 2024)
9-69432628-C-T		not specified	Uncertain significance (Oct 20, 2023)
9-69432654-C-G		not specified	Uncertain significance (Dec 03, 2021)
9-69441082-T-C		not specified	Uncertain significance (Jun 02, 2023)
9-69441102-T-C		not specified	Uncertain significance (Oct 03, 2022)
9-69441105-T-A		not specified	Uncertain significance (Oct 25, 2023)
9-69449655-C-T		not specified	Uncertain significance (Sep 10, 2024)
9-69449663-T-A		not specified	Uncertain significance (Feb 13, 2023)
9-69449666-A-C		not specified	Uncertain significance (Aug 27, 2024)
9-69452138-G-A		not specified	Uncertain significance (Dec 22, 2023)
9-69452297-T-C		not specified	Uncertain significance (Sep 30, 2024)
9-69456258-C-T		not specified	Uncertain significance (Dec 04, 2024)
9-69456321-C-T		not specified	Uncertain significance (Dec 19, 2022)
9-69456342-G-A		not specified	Uncertain significance (Aug 19, 2024)
9-69456342-G-C		not specified	Uncertain significance (Dec 05, 2024)
9-69456344-G-C		not specified	Uncertain significance (Dec 12, 2023)
9-69456353-C-T		not specified	Uncertain significance (Jul 21, 2021)
9-69456357-G-A		not specified	Uncertain significance (Nov 27, 2024)
9-69456369-C-G		not specified	Uncertain significance (Sep 27, 2024)
9-69456371-A-G		not specified	Uncertain significance (Aug 10, 2024)
9-69457109-C-T		not specified	Uncertain significance (Dec 15, 2023)
9-69457119-C-G		not specified	Uncertain significance (Jan 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APBA1	protein_coding	protein_coding	ENST00000265381	12	244777

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.537	0.463	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.23	404	551	0.733	0.0000381	5436
Missense in Polyphen		130	203	0.64039		2082
Synonymous	-0.400	271	263	1.03	0.0000231	1609
Loss of Function	4.44	8	37.2	0.215	0.00000182	416

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000280	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000885	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000332	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative function in synaptic vesicle exocytosis by binding to Munc18-1, 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;Dopamine Neurotransmitter Release Cycle;Neurotransmitter release cycle;Neurexins and neuroligins;Transmission across Chemical Synapses;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.221

Intolerance Scores

• loftool: 0.188
• rvis_EVS: -1.44
• rvis_percentile_EVS: 3.96

Haploinsufficiency Scores

• pHI: 0.134
• hipred: Y
• hipred_score: 0.749
• ghis: 0.647

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.789

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apba1
• Phenotype: 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: in utero embryonic development;intracellular protein transport;cell adhesion;chemical synaptic transmission;neurotransmitter secretion;nervous system development;locomotory behavior;axo-dendritic transport;regulation of gene expression;glutamate secretion;gamma-aminobutyric acid secretion;multicellular organism growth;protein-containing complex assembly;regulation of synaptic vesicle exocytosis
• Cellular component: nucleus;cytoplasm;Golgi apparatus;cytosol;plasma membrane;synaptic vesicle;dendritic spine;synapse;perinuclear region of cytoplasm;presynaptic active zone membrane;Schaffer collateral - CA1 synapse;glutamatergic synapse
• Molecular function: amyloid-beta binding;protein binding