APLP2

amyloid beta precursor like protein 2

Basic information

Region (hg38): 11:130068146-130144811

Previous symbols: [ "APPL2" ]

Links

ENSG00000084234 ∙ NCBI:334 ∙ OMIM:104776 ∙ HGNC:598 ∙ Uniprot:Q06481 ∙ 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 APLP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APLP2 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			54	1		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	54	2	2

Variants in APLP2

This is a list of pathogenic ClinVar variants found in the APLP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-130070075-A-C		not specified	Uncertain significance (Sep 16, 2021)
11-130109573-A-G		not specified	Uncertain significance (Sep 01, 2021)
11-130109580-A-T		not specified	Uncertain significance (Jun 16, 2023)
11-130109581-A-T		not specified	Uncertain significance (Jan 03, 2024)
11-130120717-G-A		not specified	Uncertain significance (Mar 20, 2023)
11-130120743-A-T		not specified	Uncertain significance (Nov 12, 2021)
11-130120769-G-A		not specified	Uncertain significance (Mar 16, 2022)
11-130120789-C-T		not specified	Uncertain significance (Mar 01, 2023)
11-130120802-A-T		not specified	Uncertain significance (Mar 26, 2024)
11-130121621-T-G		not specified	Uncertain significance (Feb 16, 2023)
11-130121668-G-A		not specified	Uncertain significance (Apr 01, 2024)
11-130121677-C-G		not specified	Uncertain significance (Mar 11, 2022)
11-130121762-A-G		not specified	Uncertain significance (Dec 21, 2021)
11-130121769-G-T		not specified	Uncertain significance (Mar 31, 2023)
11-130121800-G-A		not specified	Likely benign (Aug 04, 2023)
11-130122321-G-A		not specified	Uncertain significance (Apr 13, 2022)
11-130122403-G-A		not specified	Uncertain significance (Jan 07, 2022)
11-130122454-C-G		not specified	Uncertain significance (Jun 16, 2024)
11-130122469-G-C		not specified	Uncertain significance (Feb 16, 2023)
11-130122522-A-C			Benign (Mar 29, 2018)
11-130123647-C-T		not specified	Uncertain significance (Apr 27, 2023)
11-130123662-C-T		not specified	Uncertain significance (Dec 22, 2023)
11-130123663-G-A		not specified	Uncertain significance (Feb 03, 2022)
11-130123674-G-A		not specified	Uncertain significance (Jan 16, 2024)
11-130123691-G-T		not specified	Uncertain significance (Jun 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APLP2	protein_coding	protein_coding	ENST00000263574	18	74968

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.380	0.620	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00417	455	455	1.00	0.0000268	5068
Missense in Polyphen		193	206.92	0.93271		2229
Synonymous	0.0466	165	166	0.995	0.0000101	1394
Loss of Function	4.54	9	39.9	0.225	0.00000195	480

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the regulation of hemostasis. The soluble form may have inhibitory properties towards coagulation factors. May interact with cellular G-protein signaling pathways. May bind to the DNA 5'-GTCACATG-3'(CDEI box). Inhibits trypsin, chymotrypsin, plasmin, factor XIA and plasma and glandular kallikrein. Modulates the Cu/Zn nitric oxide-catalyzed autodegradation of GPC1 heparan sulfate side chains in fibroblasts (By similarity). {ECO:0000250, ECO:0000269|PubMed:8307156}.
• Pathway: Splicing factor NOVA regulated synaptic proteins;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;EGFR1;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.200

Intolerance Scores

• loftool: 0.0205
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.67

Haploinsufficiency Scores

• pHI: 0.256
• hipred: Y
• hipred_score: 0.718
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.887

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Aplp2
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; embryo 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); reproductive 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: platelet degranulation;G protein-coupled receptor signaling pathway;negative regulation of endopeptidase activity;post-translational protein modification;cellular protein metabolic process
• Cellular component: nucleus;endoplasmic reticulum lumen;plasma membrane;membrane;integral component of membrane;platelet alpha granule membrane;extracellular exosome
• Molecular function: DNA binding;serine-type endopeptidase inhibitor activity;protein binding;heparin binding;identical protein binding;transition metal ion binding