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.

not_specified (99 variants)

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. These statistics are base on transcript: NM_000004307.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			97 clinvar	2 clinvar		99
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	97	2	0

Loading clinvar variants...

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