ABL2

ABL proto-oncogene 2, non-receptor tyrosine kinase, the group of Abl family tyrosine kinases|SH2 domain containing

Basic information

Region (hg38): 1:179099330-179229684

Previous symbols: [ "ABLL" ]

Links

ENSG00000143322 ∙ NCBI:27 ∙ OMIM:164690 ∙ HGNC:77 ∙ Uniprot:P42684 ∙ 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 ABL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABL2 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			40	1	1	42
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	41	2	2

Variants in ABL2

This is a list of pathogenic ClinVar variants found in the ABL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-179103593-T-C			Benign (Apr 27, 2020)
1-179107777-G-C		not specified	Uncertain significance (Jun 29, 2023)
1-179107800-G-A		not specified	Uncertain significance (Jan 10, 2022)
1-179107978-A-T		not specified	Uncertain significance (Feb 28, 2023)
1-179108128-G-C		not specified	Uncertain significance (Feb 16, 2023)
1-179108182-C-T		not specified	Uncertain significance (May 26, 2024)
1-179108248-T-C		not specified	Uncertain significance (Jul 13, 2021)
1-179108297-C-T		not specified	Uncertain significance (Jul 11, 2023)
1-179108346-C-T		not specified	Uncertain significance (Feb 28, 2024)
1-179108370-A-G		not specified	Uncertain significance (Apr 24, 2024)
1-179108372-C-G		not specified	Uncertain significance (Dec 17, 2023)
1-179108478-T-C			Benign (Jul 01, 2023)
1-179108486-G-T		not specified	Uncertain significance (Dec 04, 2023)
1-179108535-G-A		not specified	Uncertain significance (Jan 04, 2024)
1-179108545-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-179108656-T-C		not specified	Uncertain significance (Sep 21, 2023)
1-179108707-G-C		not specified	Uncertain significance (Jan 30, 2024)
1-179108713-A-T		not specified	Uncertain significance (Jun 24, 2022)
1-179108878-T-C		not specified	Uncertain significance (May 24, 2023)
1-179108892-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-179108908-T-C		not specified	Uncertain significance (Oct 03, 2023)
1-179108917-T-A			Likely benign (Dec 01, 2022)
1-179108974-C-T		not specified	Uncertain significance (Jun 29, 2023)
1-179109043-C-G		not specified	Uncertain significance (Jun 11, 2021)
1-179109119-C-G		not specified	Uncertain significance (Oct 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABL2	protein_coding	protein_coding	ENST00000502732	12	130358

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.64e-7	1.00	125588	1	159	125748	0.000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	520	640	0.813	0.0000332	7645
Missense in Polyphen		172	287.27	0.59875		3486
Synonymous	-0.813	265	249	1.07	0.0000134	2453
Loss of Function	3.94	20	50.1	0.399	0.00000321	550

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000926	0.000926
Ashkenazi Jewish	0.00298	0.00298
East Asian	0.000217	0.000217
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000723	0.000712
Middle Eastern	0.000217	0.000217
South Asian	0.000359	0.000359
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Non-receptor tyrosine-protein kinase that plays an ABL1- overlapping role in key processes linked to cell growth and survival such as cytoskeleton remodeling in response to extracellular stimuli, cell motility and adhesion and receptor endocytosis. Coordinates actin remodeling through tyrosine phosphorylation of proteins controlling cytoskeleton dynamics like MYH10 (involved in movement); CTTN (involved in signaling); or TUBA1 and TUBB (microtubule subunits). Binds directly F-actin and regulates actin cytoskeletal structure through its F-actin- bundling activity. Involved in the regulation of cell adhesion and motility through phosphorylation of key regulators of these processes such as CRK, CRKL, DOK1 or ARHGAP35. Adhesion-dependent phosphorylation of ARHGAP35 promotes its association with RASA1, resulting in recruitment of ARHGAP35 to the cell periphery where it inhibits RHO. Phosphorylates multiple receptor tyrosine kinases like PDGFRB and other substrates which are involved in endocytosis regulation such as RIN1. In brain, may regulate neurotransmission by phosphorylating proteins at the synapse. ABL2 acts also as a regulator of multiple pathological signaling cascades during infection. Pathogens can highjack ABL2 kinase signaling to reorganize the host actin cytoskeleton for multiple purposes, like facilitating intracellular movement and host cell exit. Finally, functions as its own regulator through autocatalytic activity as well as through phosphorylation of its inhibitor, ABI1. {ECO:0000269|PubMed:15735735, ECO:0000269|PubMed:15886098, ECO:0000269|PubMed:16678104, ECO:0000269|PubMed:17306540, ECO:0000269|PubMed:18945674}.
• Pathway: Viral myocarditis - Homo sapiens (human);ErbB signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Ras Signaling;Developmental Biology;y branching of actin filaments;EGFR1;Signaling by ROBO receptors;Axon guidance;Role of ABL in ROBO-SLIT signaling (Consensus)

Recessive Scores

• pRec: 0.213

Intolerance Scores

• loftool: 0.680
• rvis_EVS: -0.99
• rvis_percentile_EVS: 8.6

Haploinsufficiency Scores

• pHI: 0.887
• hipred: Y
• hipred_score: 0.648
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.984

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abl2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo 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); reproductive 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); 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); cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: cellular protein modification process;cell adhesion;signal transduction;positive regulation of cytosolic calcium ion concentration;regulation of autophagy;positive regulation of phospholipase C activity;positive regulation of neuron projection development;peptidyl-tyrosine phosphorylation;regulation of endocytosis;cell differentiation;regulation of cell adhesion;peptidyl-tyrosine autophosphorylation;regulation of cell population proliferation;positive regulation of oxidoreductase activity;cellular response to retinoic acid;regulation of cell motility;regulation of actin cytoskeleton reorganization
• Cellular component: cytosol;actin cytoskeleton
• Molecular function: magnesium ion binding;phosphotyrosine residue binding;actin monomer binding;protein kinase activity;protein tyrosine kinase activity;non-membrane spanning protein tyrosine kinase activity;protein binding;ATP binding;manganese ion binding;actin filament binding