APPBP2

amyloid beta precursor protein binding protein 2

Basic information

Region (hg38): 17:60443158-60526242

Links

ENSG00000062725 ∙ NCBI:10513 ∙ OMIM:605324 ∙ HGNC:622 ∙ Uniprot:Q92624 ∙ 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 APPBP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APPBP2 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in APPBP2

This is a list of pathogenic ClinVar variants found in the APPBP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-60447600-A-G		not specified	Uncertain significance (Jan 17, 2024)
17-60447628-C-G		not specified	Uncertain significance (Sep 12, 2023)
17-60447661-C-T		not specified	Uncertain significance (Dec 28, 2023)
17-60447705-C-T		not specified	Uncertain significance (Sep 17, 2021)
17-60462009-G-C		not specified	Uncertain significance (Nov 14, 2023)
17-60464061-G-C		not specified	Uncertain significance (Aug 17, 2022)
17-60479182-G-A		not specified	Uncertain significance (Feb 15, 2023)
17-60479191-C-T		not specified	Uncertain significance (Dec 27, 2023)
17-60494615-T-C		not specified	Uncertain significance (Jun 18, 2021)
17-60525852-C-T		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APPBP2	protein_coding	protein_coding	ENST00000083182	13	83061

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00433	125738	0	8	125746	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.09	154	306	0.503	0.0000149	3827
Missense in Polyphen		18	92.374	0.19486		1171
Synonymous	-0.326	115	111	1.04	0.00000531	1076
Loss of Function	4.74	4	33.7	0.119	0.00000174	416

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000532	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in intracellular protein transport. May be involved in the translocation of APP along microtubules toward the cell surface. {ECO:0000269|PubMed:9843960}.
• Pathway: Regulation of Androgen receptor activity (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.776
• hipred: Y
• hipred_score: 0.717
• ghis: 0.657

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.896

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Appbp2

Gene ontology

• Biological process: intracellular protein transport;intracellular transport
• Cellular component: nucleus;cytoplasm;microtubule;microtubule associated complex;cytoplasmic vesicle membrane
• Molecular function: microtubule motor activity;protein binding