APLP1

amyloid beta precursor like protein 1

Basic information

Region (hg38): 19:35867899-35879803

Links

ENSG00000105290 ∙ NCBI:333 ∙ OMIM:104775 ∙ HGNC:597 ∙ Uniprot:P51693 ∙ 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 APLP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APLP1 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	1		34
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	1	1

Variants in APLP1

This is a list of pathogenic ClinVar variants found in the APLP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35868677-G-A		not specified	Uncertain significance (Jul 05, 2023)
19-35869689-C-T		not specified	Uncertain significance (Mar 25, 2024)
19-35869709-A-G		not specified	Uncertain significance (Nov 22, 2023)
19-35869721-G-A		not specified	Uncertain significance (May 03, 2023)
19-35869764-G-A		not specified	Uncertain significance (Mar 22, 2023)
19-35870936-C-G		not specified	Uncertain significance (Oct 26, 2021)
19-35870978-G-A		not specified	Uncertain significance (Jul 09, 2021)
19-35870995-C-A		not specified	Uncertain significance (Mar 11, 2022)
19-35871020-G-A		not specified	Likely benign (Jan 03, 2024)
19-35871293-C-G		not specified	Uncertain significance (Mar 18, 2024)
19-35871697-T-C		not specified	Uncertain significance (Dec 07, 2023)
19-35871871-C-T		not specified	Uncertain significance (Oct 02, 2023)
19-35871872-G-A		not specified	Uncertain significance (Aug 31, 2022)
19-35871880-C-T		not specified	Uncertain significance (Feb 05, 2024)
19-35871884-C-G		not specified	Uncertain significance (Dec 14, 2022)
19-35871895-G-A		not specified	Uncertain significance (Jul 06, 2021)
19-35871943-G-T		not specified	Uncertain significance (Feb 26, 2024)
19-35871973-G-A		not specified	Uncertain significance (May 11, 2022)
19-35871994-G-A		not specified	Uncertain significance (Jan 26, 2022)
19-35872540-A-G		not specified	Uncertain significance (Aug 19, 2021)
19-35872580-C-T			Benign (Apr 20, 2018)
19-35873645-C-A		not specified	Uncertain significance (Nov 14, 2023)
19-35873673-C-A		not specified	Uncertain significance (Jul 06, 2021)
19-35873693-G-A		not specified	Uncertain significance (Mar 21, 2023)
19-35874544-C-G		not specified	Uncertain significance (Oct 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APLP1	protein_coding	protein_coding	ENST00000221891	17	11893

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.122	0.878	125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	324	392	0.828	0.0000246	4157
Missense in Polyphen		137	179.06	0.76512		1941
Synonymous	-1.17	177	158	1.12	0.0000101	1348
Loss of Function	4.17	9	36.0	0.250	0.00000188	374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000262	0.000262
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000799	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.0000655	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in postsynaptic function. The C-terminal gamma-secretase processed fragment, ALID1, activates transcription activation through APBB1 (Fe65) binding (By similarity). Couples to JIP signal transduction through C-terminal binding. May interact with cellular G-protein signaling pathways. Can regulate neurite outgrowth through binding to components of the extracellular matrix such as heparin and collagen I. {ECO:0000250}.

Recessive Scores

• pRec: 0.617

Intolerance Scores

• loftool: 0.0546
• rvis_EVS: -0.68
• rvis_percentile_EVS: 15.36

Haploinsufficiency Scores

• pHI: 0.334
• hipred: Y
• hipred_score: 0.597
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.760

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Aplp1
• 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

Gene ontology

• Biological process: endocytosis;apoptotic process;cell adhesion;nervous system development;animal organ morphogenesis;cellular response to norepinephrine stimulus;negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway
• Cellular component: basement membrane;plasma membrane;integral component of membrane;perinuclear region of cytoplasm
• Molecular function: protein binding;heparin binding;alpha-2A adrenergic receptor binding;alpha-2B adrenergic receptor binding;alpha-2C adrenergic receptor binding;identical protein binding;transition metal ion binding