APBB3

amyloid beta precursor protein binding family B member 3, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 5:140558268-140564781

Links

ENSG00000113108 ∙ NCBI:10307 ∙ OMIM:602711 ∙ HGNC:20708 ∙ Uniprot:O95704 ∙ 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 APBB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APBB3 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			33	2		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	3	0

Variants in APBB3

This is a list of pathogenic ClinVar variants found in the APBB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140558617-G-A		not specified	Uncertain significance (Jun 03, 2024)
5-140558646-C-G		not specified	Uncertain significance (Oct 06, 2022)
5-140558646-C-T		not specified	Uncertain significance (Sep 22, 2022)
5-140558653-G-C		not specified	Uncertain significance (Jun 13, 2022)
5-140558664-C-T		not specified	Uncertain significance (Jun 29, 2023)
5-140558671-C-T		not specified	Uncertain significance (Nov 22, 2021)
5-140558707-G-A		not specified	Uncertain significance (Mar 15, 2024)
5-140558757-C-T		not specified	Uncertain significance (Oct 26, 2022)
5-140558782-C-T		not specified	Uncertain significance (Sep 10, 2024)
5-140560344-C-T		not specified	Uncertain significance (Jul 14, 2021)
5-140560392-C-A		not specified	Uncertain significance (Jan 23, 2024)
5-140560392-C-T		not specified	Uncertain significance (Dec 27, 2023)
5-140560420-T-C		not specified	Uncertain significance (Feb 12, 2024)
5-140560429-C-T		not specified	Uncertain significance (Sep 01, 2021)
5-140560467-C-T		not specified	Uncertain significance (May 24, 2023)
5-140560645-G-A			Likely benign (Apr 01, 2022)
5-140560703-C-T		not specified	Likely benign (Oct 12, 2022)
5-140560704-G-A		not specified	Uncertain significance (Oct 03, 2024)
5-140560713-T-A		not specified	Uncertain significance (Aug 11, 2024)
5-140560716-C-T		not specified	Likely benign (Mar 01, 2024)
5-140561027-T-C		not specified	Uncertain significance (Jul 08, 2021)
5-140561051-A-G		not specified	Uncertain significance (Dec 13, 2022)
5-140561060-C-T		not specified	Uncertain significance (Aug 21, 2023)
5-140561069-G-C		not specified	Uncertain significance (Dec 27, 2022)
5-140561072-C-T		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APBB3	protein_coding	protein_coding	ENST00000354402	13	35485

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.08e-10	0.826	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.814	261	301	0.868	0.0000175	3204
Missense in Polyphen		132	153.96	0.85735		1766
Synonymous	0.0250	110	110	0.997	0.00000584	1013
Loss of Function	1.67	19	28.6	0.664	0.00000145	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000520	0.000514
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.000109	0.000109
South Asian	0.000362	0.000359
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modulate the internalization of amyloid-beta precursor protein.

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.926
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.13

Haploinsufficiency Scores

• pHI: 0.479
• hipred: N
• hipred_score: 0.484
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.304

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apbb3

Gene ontology

• Biological process: regulation of transcription, DNA-templated
• Cellular component: nucleus;cytoplasm;cytosol;actin cytoskeleton
• Molecular function: amyloid-beta binding;protein binding;transcription factor binding