ABI1

abl interactor 1

Basic information

Region (hg38): 10:26746592-26861087

Previous symbols: [ "SSH3BP1" ]

Links

ENSG00000136754 ∙ NCBI:10006 ∙ OMIM:603050 ∙ HGNC:11320 ∙ Uniprot:Q8IZP0 ∙ 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 ABI1 gene.

• Inborn genetic diseases (7 variants)
• not provided (4 variants)
• Deafness-encephaloneuropathy-obesity-valvulopathy syndrome (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABI1 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	2
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	3		5
Total	0	0	9	4	1

Variants in ABI1

This is a list of pathogenic ClinVar variants found in the ABI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-26746610-AT-A			Likely benign (Sep 18, 2020)
10-26746620-A-G		Deafness-encephaloneuropathy-obesity-valvulopathy syndrome	Uncertain significance (Jan 13, 2018)
10-26746630-T-G		Deafness-encephaloneuropathy-obesity-valvulopathy syndrome	Benign/Likely benign (Oct 08, 2021)
10-26746735-T-C		Deafness-encephaloneuropathy-obesity-valvulopathy syndrome	Uncertain significance (Jan 12, 2018)
10-26746737-A-T		Deafness-encephaloneuropathy-obesity-valvulopathy syndrome	Likely benign (Jan 13, 2018)
10-26751654-T-C		not specified	Uncertain significance (Mar 01, 2024)
10-26751707-T-G			Benign (Jun 20, 2018)
10-26755734-A-C		not specified	Uncertain significance (Feb 28, 2023)
10-26759097-T-C		not specified	Uncertain significance (Dec 17, 2023)
10-26759181-C-G		not specified	Uncertain significance (Nov 29, 2023)
10-26763907-G-A		not specified	Uncertain significance (Mar 08, 2024)
10-26763933-C-A		not specified	Uncertain significance (May 18, 2023)
10-26765246-A-G			Likely benign (Jul 01, 2022)
10-26765301-C-A		not specified	Uncertain significance (Sep 23, 2023)
10-26768877-A-C		not specified	Uncertain significance (Apr 05, 2023)
10-26768925-T-C		not specified	Uncertain significance (Mar 21, 2023)
10-26768966-T-C		not specified	Uncertain significance (Jan 05, 2022)
10-26777115-G-A		not specified	Uncertain significance (Nov 09, 2023)
10-26860754-T-C		not specified	Uncertain significance (Jul 26, 2022)
10-26860838-T-A		not specified	Uncertain significance (Nov 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABI1	protein_coding	protein_coding	ENST00000376142	12	114495

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.639	0.361	125696	0	4	125700	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.09	182	281	0.648	0.0000138	3268
Missense in Polyphen		49	97.349	0.50334		1215
Synonymous	-0.195	101	98.5	1.03	0.00000481	1055
Loss of Function	3.72	5	25.1	0.199	0.00000135	291

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000207	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000395	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act in negative regulation of cell growth and transformation by interacting with nonreceptor tyrosine kinases ABL1 and/or ABL2. May play a role in regulation of EGF-induced Erk pathway activation. Involved in cytoskeletal reorganization and EGFR signaling. Together with EPS8 participates in transduction of signals from Ras to Rac. In vitro, a trimeric complex of ABI1, EPS8 and SOS1 exhibits Rac specific guanine nucleotide exchange factor (GEF) activity and ABI1 seems to act as an adapter in the complex. Regulates ABL1/c-Abl-mediated phosphorylation of ENAH. Recruits WASF1 to lamellipodia and there seems to regulate WASF1 protein level. In brain, seems to regulate the dendritic outgrowth and branching as well as to determine the shape and number of synaptic contacts of developing neurons. {ECO:0000269|PubMed:11003655, ECO:0000269|PubMed:18328268}.
• Disease: DISEASE: Note=A chromosomal aberration involving ABI1 is a cause of acute leukemias. Translocation t(10;11)(p11.2;q23) with KMT2A/MLL1. ABI1 isoform 2 was found to be present in acute leukemia KMT2A/MLL1-ABI1 fusion transcript. {ECO:0000269|PubMed:9694699}.
• Pathway: EGF-EGFR Signaling Pathway;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;EGFR1;Regulation of RAC1 activity;ErbB1 downstream signaling;Regulation of actin dynamics for phagocytic cup formation;Signaling by VEGF;Signaling by Receptor Tyrosine Kinases;Stabilization and expansion of the E-cadherin adherens junction;RAC1 signaling pathway;Alpha4 beta1 integrin signaling events;PDGFR-beta signaling pathway;E-cadherin signaling in the nascent adherens junction (Consensus)

Recessive Scores

• pRec: 0.297

Intolerance Scores

• loftool: 0.0520
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.524
• hipred: Y
• hipred_score: 0.745
• ghis: 0.662

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.707

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abi1
• 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); immune system phenotype; embryo phenotype; growth/size/body region phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: somitogenesis;transmembrane receptor protein tyrosine kinase signaling pathway;actin polymerization or depolymerization;negative regulation of cell population proliferation;viral process;peptidyl-tyrosine phosphorylation;megakaryocyte development;Fc-gamma receptor signaling pathway involved in phagocytosis;vascular endothelial growth factor receptor signaling pathway;dendrite morphogenesis;positive regulation of protein tyrosine kinase activity;lamellipodium morphogenesis
• Cellular component: nucleus;endoplasmic reticulum;cytosol;cytoskeleton;postsynaptic density;lamellipodium;cell junction;growth cone;SCAR complex;filopodium tip;postsynaptic membrane;extracellular exosome
• Molecular function: protein binding;cytoskeletal protein binding;SH3 domain binding;protein tyrosine kinase activator activity;cadherin binding