APBA3

amyloid beta precursor protein binding family A member 3, the group of PDZ domain containing

Basic information

Region (hg38): 19:3750772-3761692

Links

ENSG00000011132 ∙ NCBI:9546 ∙ OMIM:604262 ∙ HGNC:580 ∙ Uniprot:O96018 ∙ 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 APBA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APBA3 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
missense			63	5		68
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	63	5	1

Variants in APBA3

This is a list of pathogenic ClinVar variants found in the APBA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-3751030-A-G		not specified	Uncertain significance (Sep 04, 2024)
19-3751034-A-G		not specified	Uncertain significance (Oct 20, 2023)
19-3751037-C-T		not specified	Uncertain significance (Dec 22, 2023)
19-3751057-A-G		not specified	Uncertain significance (Jan 30, 2024)
19-3751064-G-A		not specified	Uncertain significance (Jun 05, 2023)
19-3751075-G-A		not specified	Uncertain significance (May 18, 2022)
19-3751191-C-T		not specified	Uncertain significance (May 31, 2023)
19-3751196-T-C		not specified	Uncertain significance (Jul 31, 2024)
19-3751241-A-C		not specified	Uncertain significance (Aug 17, 2021)
19-3751247-C-G		not specified	Uncertain significance (Jan 16, 2024)
19-3751264-A-C		not specified	Uncertain significance (Mar 27, 2023)
19-3751272-G-A		not specified	Uncertain significance (May 31, 2023)
19-3751295-C-T		not specified	Uncertain significance (Oct 10, 2023)
19-3751299-C-T		not specified	Uncertain significance (Apr 20, 2023)
19-3751301-G-A		not specified	Uncertain significance (Nov 13, 2023)
19-3751313-C-T		not specified	Uncertain significance (Aug 12, 2024)
19-3751438-C-T		not specified	Uncertain significance (Nov 26, 2024)
19-3751466-C-T		not specified	Uncertain significance (Nov 13, 2024)
19-3751478-G-A		not specified	Uncertain significance (Dec 27, 2023)
19-3751480-C-T		not specified	Uncertain significance (Nov 09, 2021)
19-3751492-G-A		not specified	Uncertain significance (May 24, 2024)
19-3751517-C-T		not specified	Uncertain significance (Feb 10, 2022)
19-3751532-C-A		not specified	Uncertain significance (May 05, 2023)
19-3751537-G-A		not specified	Uncertain significance (Feb 27, 2023)
19-3751549-G-A		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APBA3	protein_coding	protein_coding	ENST00000316757	10	10881

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.07e-12	0.121	125376	1	307	125684	0.00123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.236	376	363	1.03	0.0000240	3613
Missense in Polyphen		130	135.64	0.95839		1356
Synonymous	-0.136	165	163	1.01	0.0000118	1215
Loss of Function	0.661	20	23.5	0.853	0.00000142	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000827	0.000779
Ashkenazi Jewish	0.00	0.00
East Asian	0.00608	0.00573
Finnish	0.0000734	0.0000462
European (Non-Finnish)	0.000491	0.000458
Middle Eastern	0.00608	0.00573
South Asian	0.00424	0.00403
Other	0.00106	0.000979

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modulate processing of the amyloid-beta precursor protein (APP) and hence formation of APP-beta. May enhance the activity of HIF1A in macrophages by inhibiting the activity of HIF1AN. {ECO:0000269|PubMed:19726677}.
• Pathway: Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.892
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.27

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.441
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.884

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apba3
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; normal 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); hematopoietic system 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;regulation of gene expression;protein transport;negative regulation of catalytic activity
• Cellular component: cytoplasm;plasma membrane;dendritic spine;synapse;perinuclear region of cytoplasm
• Molecular function: amyloid-beta binding;enzyme inhibitor activity;protein binding;enzyme binding