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Intellectual disability

Gene: ITFG2

Amber List (moderate evidence)

ITFG2 (integrin alpha FG-GAP repeat containing 2)
EnsemblGeneIds (GRCh38): ENSG00000111203
EnsemblGeneIds (GRCh37): ENSG00000111203
OMIM: 617421, Gene2Phenotype
ITFG2 is in 1 panel

2 reviews

Arina Puzriakova (Genomics England Curator)

Comment on list classification: New gene added by Konstantinos Varvagiannis. Rating Amber as ITFG2 can only be classified as a possible candidate gene based present evidence. Clinical and pedigree details are limited and there is no supporting functional data. Additional cases required to corroborate this gene-disease association.
Created: 21 Dec 2020, 10:58 a.m. | Last Modified: 21 Dec 2020, 10:58 a.m.
Panel Version: 3.662

Konstantinos Varvagiannis (Other)

I don't know

ITFG2 was suggested to be a candidate gene for autosomal recessive ID in the study by Harripaul et al (2018 - PMID: 28397838). The authors performed microarray and exome sequencing in 192 consanguineous families and identified a homozygous ITGF2 stopgain variant (NM_018463.3:c.472G>T / p.Glu158*) along with 3 additional variants segregating with ID within an investigated family (PK51).

Cheema et al (2020 - report briefly on a male, born to consanguineous parents presenting with NDD, seizures, regression and ataxia. There was a similarly affected female sibling. Evaluation of ROH revealed a homozygous ITFG2 nonsense variant [NM_018463.3:c.361C>T / p.(Gln121*)]. Families in this study were investigated by trio WES or WGS.

Evaluation of data of the same lab revealed 3 additional unrelated subjects with overlapping phenotypes, notably NDD and ataxia. These individuals were - each - homozygous for pLoF variants [NM_018463.3:c.848-1G>A; NM_018463.3:c.704dupC, p.(Ala236fs), NM_018463.3:c.1000_1001delAT, p.(Ile334fs)].

As discussed in OMIM, ITFG2 encodes a subunit of the KICSTOR protein complex, having a role in regulating nutrient sensing by MTOR complex-1 (Wolfson et al 2017 - PMID : 28199306).

Please consider inclusion in the ID panel with amber rating, pending further details.
Sources: Literature
Created: 10 Oct 2020, 10:46 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Neurodevelopmental abnormality; Intellectual disability; Developmental regression; Ataxia


  • 28397838


Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
  • Expert Review Amber
  • Neurodevelopmental abnormality
  • Intellectual disability
  • Developmental regression
  • Ataxia
Clinvar variants
Variants in ITFG2
Panels with this gene

History Filter Activity

21 Dec 2020, Gel status: 2

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: ITFG2 were set to 28397838;

21 Dec 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: itfg2 has been classified as Amber List (Moderate Evidence).

10 Oct 2020, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes, Set penetrance

Konstantinos Varvagiannis (Other)

gene: ITFG2 was added gene: ITFG2 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: ITFG2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ITFG2 were set to 28397838; Phenotypes for gene: ITFG2 were set to Neurodevelopmental abnormality; Intellectual disability; Developmental regression; Ataxia Penetrance for gene: ITFG2 were set to Complete Review for gene: ITFG2 was set to AMBER