ABI2

abl interactor 2, the group of SCAR/WAVE complex

Basic information

Region (hg38): 2:203328279-203447728

Links

ENSG00000138443 ∙ NCBI:10152 ∙ OMIM:606442 ∙ HGNC:24011 ∙ Uniprot:Q9NYB9 ∙ 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 ABI2 gene.

• Inborn genetic diseases (37 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABI2 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			29	1		30
Total	0	0	37	1	0

Variants in ABI2

This is a list of pathogenic ClinVar variants found in the ABI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-203328552-C-T		not specified	Uncertain significance (Jan 09, 2024)
2-203367010-G-A		not specified	Uncertain significance (Dec 09, 2023)
2-203367027-A-G		not specified	Uncertain significance (Jun 07, 2023)
2-203380266-A-G		not specified	Uncertain significance (Apr 11, 2023)
2-203380304-G-T		not specified	Uncertain significance (Jul 11, 2023)
2-203380343-A-G		ABI2-related disorder • not specified	Conflicting classifications of pathogenicity (Aug 29, 2022)
2-203395693-C-T		not specified	Uncertain significance (Jan 30, 2024)
2-203395741-A-G		not specified	Uncertain significance (Aug 02, 2022)
2-203402697-T-A		not specified	Uncertain significance (Aug 19, 2023)
2-203402707-G-A		not specified	Uncertain significance (Jan 08, 2024)
2-203411347-T-A		not specified	Uncertain significance (Feb 10, 2022)
2-203427242-A-C		not specified	Uncertain significance (Apr 25, 2022)
2-203427323-G-A		not specified	Uncertain significance (Jun 30, 2022)
2-203439498-C-T		not specified	Uncertain significance (May 02, 2023)
2-203439524-A-T		not specified	Uncertain significance (Jun 28, 2022)
2-203439579-G-A		not specified	Uncertain significance (Dec 19, 2022)
2-203439796-G-A		not specified	Uncertain significance (Aug 23, 2021)
2-203439819-C-T		not specified	Uncertain significance (Jan 20, 2023)
2-203439855-G-C		not specified	Uncertain significance (Jun 12, 2023)
2-203439900-G-C		not specified	Uncertain significance (Dec 13, 2023)
2-203439933-G-C		not specified	Uncertain significance (Sep 21, 2023)
2-203440009-C-T		not specified	Likely benign (Dec 11, 2023)
2-203440042-C-T		not specified	Uncertain significance (Mar 24, 2023)
2-203440120-G-T		not specified	Uncertain significance (Sep 14, 2022)
2-203440132-G-A		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABI2	protein_coding	protein_coding	ENST00000261017	10	119505

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.431	0.569	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.25	163	266	0.612	0.0000138	3070
Missense in Polyphen		53	111.87	0.47375		1295
Synonymous	1.02	78	90.4	0.863	0.00000460	950
Loss of Function	3.46	5	22.9	0.219	0.00000130	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000289	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of actin cytoskeleton dynamics underlying cell motility and adhesion. Functions as a component of the WAVE complex, which activates actin nucleating machinery Arp2/3 to drive lamellipodia formation (PubMed:21107423). Acts as regulator and substrate of nonreceptor tyrosine kinases ABL1 and ABL2 involved in processes linked to cell growth and differentiation. Positively regulates ABL1-mediated phosphorylation of ENAH, which is required for proper polymerization of nucleated actin filaments at the leading edge (PubMed:7590236, PubMed:8649853, PubMed:10498863). Contributes to the regulation of actin assembly at the tips of neuron projections. In particular, controls dendritic spine morphogenesis and may promote dendritic spine specification toward large mushroom-type spines known as repositories of memory in the brain (By similarity). In hippocampal neurons, may mediate actin-dependent BDNF-NTRK2 early endocytic trafficking that triggers dendrite outgrowth (By similarity). Participates in ocular lens morphogenesis, likely by regulating lamellipodia-driven adherens junction formation at the epithelial cell-secondary lens fiber interface (By similarity). Also required for nascent adherens junction assembly in epithelial cells (PubMed:15572692). {ECO:0000250|UniProtKB:P62484, ECO:0000269|PubMed:10498863, ECO:0000269|PubMed:15572692, ECO:0000269|PubMed:21107423, ECO:0000269|PubMed:7590236, ECO:0000269|PubMed:8649853}.
• Pathway: Regulation of actin cytoskeleton - Homo sapiens (human);Regulation of Actin Cytoskeleton;Signal Transduction;VEGFA-VEGFR2 Pathway;Fcgamma receptor (FCGR) dependent phagocytosis;Innate Immune System;Immune System;RHO GTPases Activate WASPs and WAVEs;RHO GTPase Effectors;Signaling by Rho GTPases;Regulation of actin dynamics for phagocytic cup formation;Signaling by VEGF;Signaling by Receptor Tyrosine Kinases;RAC1 signaling pathway (Consensus)

Recessive Scores

• pRec: 0.192

Intolerance Scores

• loftool: 0.181
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.490
• hipred: Y
• hipred_score: 0.748
• ghis: 0.663

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abi2
• Phenotype: cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune 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); vision/eye phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: cytoskeleton organization;nervous system development;actin polymerization or depolymerization;viral process;cell migration;Rac protein signal transduction;peptidyl-tyrosine phosphorylation;positive regulation of Arp2/3 complex-mediated actin nucleation
• Cellular component: nucleus;cytoplasm;cytosol;cytoskeleton;adherens junction;lamellipodium;SCAR complex;filopodium tip
• Molecular function: DNA binding;protein binding;cytoskeletal adaptor activity;SH3 domain binding;kinase binding;ubiquitin protein ligase binding;Rac GTPase binding;proline-rich region binding