ITFG2

integrin alpha FG-GAP repeat containing 2, the group of KICSTOR complex

Basic information

Region (hg38): 12:2812622-2859791

Previous symbols: [ "FGGAP1" ]

Links

ENSG00000111203 ∙ NCBI:55846 ∙ OMIM:617421 ∙ HGNC:30879 ∙ Uniprot:Q969R8 ∙ 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 ITFG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITFG2 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			39	1		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding			40	4	4	48
Total	0	1	79	5	4

Variants in ITFG2

This is a list of pathogenic ClinVar variants found in the ITFG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-2812770-G-C		not specified	Uncertain significance (Apr 15, 2024)
12-2812797-G-A		not specified	Uncertain significance (Dec 02, 2022)
12-2812827-A-G		not specified	Uncertain significance (Feb 12, 2024)
12-2812853-T-A		not specified	Uncertain significance (Nov 25, 2024)
12-2817235-G-T		not specified	Uncertain significance (Nov 14, 2023)
12-2817245-A-T		not specified	Uncertain significance (Feb 06, 2025)
12-2817248-C-T		not specified	Uncertain significance (Aug 02, 2021)
12-2817272-A-G		not specified	Uncertain significance (Mar 25, 2024)
12-2817274-A-G		not specified	Uncertain significance (Mar 19, 2024)
12-2817283-A-G		not specified	Uncertain significance (Aug 08, 2022)
12-2817917-C-G		not specified	Uncertain significance (Feb 11, 2025)
12-2817934-T-A		not specified	Uncertain significance (Aug 02, 2023)
12-2818151-G-T		not specified	Uncertain significance (Dec 27, 2023)
12-2818163-G-T		not specified	Uncertain significance (Feb 06, 2025)
12-2818164-C-T		not specified	Uncertain significance (Feb 06, 2025)
12-2818175-G-A		not specified	Uncertain significance (Jul 30, 2024)
12-2818212-A-G		not specified	Uncertain significance (Apr 29, 2024)
12-2818218-G-A		not specified	Uncertain significance (Jul 25, 2023)
12-2818218-G-T		not specified	Uncertain significance (Apr 11, 2023)
12-2818256-G-A		not specified	Uncertain significance (Apr 14, 2023)
12-2818271-G-A		not specified	Uncertain significance (Apr 19, 2023)
12-2820101-G-A		not specified	Uncertain significance (Dec 06, 2021)
12-2820104-A-G			Uncertain significance (Nov 16, 2024)
12-2820116-G-C		not specified	Uncertain significance (May 26, 2024)
12-2820746-T-A		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITFG2	protein_coding	protein_coding	ENST00000228799	12	47170

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.48e-8	0.902	125696	0	51	125747	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.801	233	270	0.863	0.0000156	2904
Missense in Polyphen		68	87.173	0.78006		930
Synonymous	0.831	97	108	0.898	0.00000629	893
Loss of Function	1.75	16	25.5	0.626	0.00000136	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.000829	0.000816
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000221	0.000211
Middle Eastern	0.000829	0.000816
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As part of the KICSTOR complex functions in the amino acid-sensing branch of the TORC1 signaling pathway. Recruits, in an amino acid-independent manner, the GATOR1 complex to the lysosomal membranes and allows its interaction with GATOR2 and the RAG GTPases. Functions upstream of the RAG GTPases and is required to negatively regulate mTORC1 signaling in absence of amino acids. In absence of the KICSTOR complex mTORC1 is constitutively localized to the lysosome and activated. The KICSTOR complex is also probably involved in the regulation of mTORC1 by glucose. {ECO:0000269|PubMed:28199306}.

Recessive Scores

• pRec: 0.0891

Intolerance Scores

• loftool: 0.492
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.68

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.411
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.943

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Itfg2
• Phenotype: renal/urinary system phenotype; immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: germinal center B cell differentiation;cellular response to amino acid starvation;cellular response to glucose starvation;negative regulation of TORC1 signaling
• Cellular component: nucleoplasm;lysosomal membrane;cytosol;KICSTOR complex