APBB1IP

amyloid beta precursor protein binding family B member 1 interacting protein, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 10:26438341-26568449

Links

ENSG00000077420 ∙ NCBI:54518 ∙ OMIM:609036 ∙ HGNC:17379 ∙ Uniprot:Q7Z5R6 ∙ 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 APBB1IP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APBB1IP 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				2	1	3
missense			34	1	3	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	3	4

Variants in APBB1IP

This is a list of pathogenic ClinVar variants found in the APBB1IP region.

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

Position	Type	Phenotype	Significance	ClinVar
10-26492359-G-A		not specified	Uncertain significance (Dec 22, 2023)
10-26496329-C-T		not specified	Uncertain significance (Sep 27, 2022)
10-26496352-G-A		not specified	Uncertain significance (Jun 11, 2021)
10-26496358-T-C		not specified	Uncertain significance (Oct 27, 2021)
10-26500878-G-A		not specified	Uncertain significance (Oct 03, 2023)
10-26500907-C-G		not specified	Uncertain significance (Feb 05, 2024)
10-26500965-A-G		not specified	Uncertain significance (Dec 08, 2023)
10-26503241-G-A			Likely benign (Aug 01, 2022)
10-26511766-T-C		not specified	Uncertain significance (Aug 02, 2023)
10-26511839-C-T			Benign (Oct 24, 2017)
10-26511892-C-T		not specified	Uncertain significance (Jan 31, 2024)
10-26513544-T-C		not specified	Uncertain significance (Mar 11, 2022)
10-26533498-T-G		not specified	Uncertain significance (Jan 10, 2022)
10-26536096-T-C		not specified	Uncertain significance (Sep 13, 2023)
10-26541598-C-T		not specified	Uncertain significance (Jul 19, 2022)
10-26541616-A-C		not specified	Uncertain significance (Jan 24, 2024)
10-26541676-A-G		not specified	Uncertain significance (Dec 13, 2023)
10-26560760-C-T			Benign (Oct 24, 2017)
10-26560815-A-G		not specified	Uncertain significance (Nov 28, 2023)
10-26560836-C-T		not specified	Uncertain significance (Aug 22, 2023)
10-26562337-G-A		not specified	Uncertain significance (May 29, 2024)
10-26562338-G-A		not specified	Uncertain significance (Nov 20, 2023)
10-26562344-C-T		not specified	Uncertain significance (Apr 12, 2024)
10-26566998-C-T		not specified	Uncertain significance (Oct 05, 2022)
10-26567016-A-C		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APBB1IP	protein_coding	protein_coding	ENST00000376236	13	129601

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.854	0.146	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	253	317	0.797	0.0000155	4284
Missense in Polyphen		84	113.25	0.74172		1475
Synonymous	-1.68	146	122	1.19	0.00000621	1306
Loss of Function	4.06	5	28.3	0.176	0.00000134	362

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000624	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000334	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Appears to function in the signal transduction from Ras activation to actin cytoskeletal remodeling. Suppresses insulin- induced promoter activities through AP1 and SRE. Mediates Rap1- induced adhesion. {ECO:0000269|PubMed:14530287, ECO:0000269|PubMed:15469846}.
• Pathway: Platelet activation - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);TYROBP Causal Network;MAP2K and MAPK activation;Disease;Signal Transduction;GRB2:SOS provides linkage to MAPK signaling for Integrins ;p130Cas linkage to MAPK signaling for integrins;Integrin alphaIIb beta3 signaling;Platelet Aggregation (Plug Formation);Platelet activation, signaling and aggregation;Integrin signaling;Hemostasis;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Signaling by RAS mutants;Signaling by high-kinase activity BRAF mutants;Signaling by moderate kinase activity BRAF mutants;Paradoxical activation of RAF signaling by kinase inactive BRAF;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.403
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.0911
• hipred: Y
• hipred_score: 0.822
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.484

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apbb1ip

Gene ontology

• Biological process: T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell;signal transduction;positive regulation of cell adhesion
• Cellular component: cytosol;cytoskeleton;plasma membrane;focal adhesion;lamellipodium;T cell receptor complex
• Molecular function: protein binding