APBB2

amyloid beta precursor protein binding family B member 2

Basic information

Region (hg38): 4:40810027-41216714

Links

ENSG00000163697 ∙ NCBI:323 ∙ OMIM:602710 ∙ HGNC:582 ∙ Uniprot:Q92870 ∙ 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 APBB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APBB2 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						0
missense			44			44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	44	0	0

Variants in APBB2

This is a list of pathogenic ClinVar variants found in the APBB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-40816141-G-A		not specified	Uncertain significance (Jun 05, 2023)
4-40816192-G-A		not specified	Uncertain significance (Dec 19, 2022)
4-40816195-G-A		not specified	Uncertain significance (Oct 26, 2022)
4-40816199-G-A		not specified	Uncertain significance (Jan 02, 2024)
4-40816205-G-C		not specified	Uncertain significance (Mar 20, 2023)
4-40821893-T-A		not specified	Uncertain significance (Jan 12, 2024)
4-40823649-C-T		not specified	Uncertain significance (Dec 21, 2023)
4-40823714-G-A		not specified	Uncertain significance (Apr 15, 2024)
4-40825926-C-T		not specified	Uncertain significance (Sep 29, 2023)
4-40827150-G-C		not specified	Uncertain significance (Nov 03, 2023)
4-40827165-T-C		not specified	Uncertain significance (Jun 17, 2022)
4-40830468-A-G		not specified	Uncertain significance (Aug 12, 2021)
4-40890394-C-T		not specified	Uncertain significance (Jul 05, 2023)
4-40890404-C-T		not specified	Uncertain significance (Oct 14, 2023)
4-40893294-T-G		not specified	Uncertain significance (Jul 16, 2021)
4-40893354-C-T		not specified	Uncertain significance (Oct 25, 2023)
4-40893360-C-T		not specified	Uncertain significance (Apr 13, 2022)
4-40893369-C-T		not specified	Uncertain significance (Nov 30, 2021)
4-40934663-A-T		not specified	Uncertain significance (Oct 12, 2021)
4-40944918-A-G		not specified	Uncertain significance (Mar 22, 2022)
4-40944921-C-G		not specified	Uncertain significance (Dec 28, 2022)
4-40944945-C-T		not specified	Uncertain significance (Jun 21, 2023)
4-40944975-G-C		not specified	Uncertain significance (Sep 15, 2021)
4-40945005-C-T		not specified	Uncertain significance (Aug 22, 2023)
4-40945073-G-A		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APBB2	protein_coding	protein_coding	ENST00000508593	14	406688

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0652	0.935	124772	0	29	124801	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.12	320	446	0.717	0.0000262	5000
Missense in Polyphen		119	203.05	0.58607		2207
Synonymous	0.187	176	179	0.982	0.0000118	1487
Loss of Function	4.26	10	38.5	0.260	0.00000229	406

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000220	0.000220
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.000150	0.000150
Middle Eastern	0.000111	0.000111
South Asian	0.0000654	0.0000654
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.237

Intolerance Scores

• loftool: 0.741
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.16

Haploinsufficiency Scores

• pHI: 0.408
• hipred: Y
• hipred_score: 0.756
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.921

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apbb2
• Phenotype: cellular phenotype; homeostasis/metabolism 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); growth/size/body region phenotype; 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: neuron migration;regulation of transcription, DNA-templated;cell cycle arrest;axon guidance;extracellular matrix organization;negative regulation of cell growth;intracellular signal transduction;positive regulation of apoptotic process;negative regulation of apoptotic process
• Cellular component: nucleus;cytoplasm;membrane;lamellipodium;growth cone;synapse
• Molecular function: amyloid-beta binding;protein binding;transcription factor binding