NM_002074.5(GNB1):c.239T>C (p.Ile80Thr) AND Intellectual disability, autosomal dominant 42
- Germline classification:
- Pathogenic/Likely pathogenic (15 submissions)
- Last evaluated:
- Apr 4, 2024
- Review status:
- 2 stars out of maximum of 4 starscriteria provided, multiple submitters, no conflicts
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV000225179.36
Allele description [Variation Report for NM_002074.5(GNB1):c.239T>C (p.Ile80Thr)]
NM_002074.5(GNB1):c.239T>C (p.Ile80Thr)
- Gene:
- GNB1:G protein subunit beta 1 [Gene - OMIM - HGNC]
- Variant type:
- single nucleotide variant
- Cytogenetic location:
- 1p36.33
- Genomic location:
- Preferred name:
- NM_002074.5(GNB1):c.239T>C (p.Ile80Thr)
- Other names:
- NM_002074.5(GNB1):c.239T>C
- HGVS:
- NC_000001.11:g.1806503A>G
- NG_047052.1:g.89615T>C
- NM_001282538.2:c.-62T>C
- NM_001282539.2:c.239T>C
- NM_002074.5:c.239T>CMANE SELECT
- NP_001269468.1:p.Ile80Thr
- NP_001269468.1:p.Ile80Thr
- NP_002065.1:p.Ile80Thr
- NC_000001.10:g.1737942A>G
- NM_001282539.1:c.239T>C
- NM_002074.3:c.239T>C
- NM_002074.4:c.239T>C
- P62873:p.Ile80Thr
This HGVS expression did not pass validation- Protein change:
- I80T; ILE80THR
- Links:
- UniProtKB: P62873#VAR_076648; OMIM: 139380.0002; dbSNP: rs752746786
- NCBI 1000 Genomes Browser:
- rs752746786
- Molecular consequence:
- NM_001282538.2:c.-62T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001282539.2:c.239T>C - missense variant - [Sequence Ontology: SO:0001583]
- NM_002074.5:c.239T>C - missense variant - [Sequence Ontology: SO:0001583]
- Functional consequence:
- effect on protein interaction [Variation Ontology: 0058]
- Observations:
- 3
Condition(s)
Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000282059 | OMIM | no assertion criteria provided | Pathogenic (Nov 2, 2021) | unknown | literature only | |
SCV001150119 | Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München | criteria provided, single submitter (Classification criteria August 2017) | Pathogenic (Aug 19, 2019) | de novo | clinical testing | |
SCV001364389 | Department of Paediatrics and Adolescent Medicine, The University of Hong Kong | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jun 2, 2020) | unknown | research | |
SCV001427084 | Clinical Genomics Program, Stanford Medicine | no assertion criteria provided | Pathogenic (Sep 26, 2019) | germline | clinical testing | |
SCV001440423 | Institute of Human Genetics, University of Leipzig Medical Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Feb 20, 2024) | unknown | clinical testing | |
SCV001478316 | GeneReviews | no classification provided | not provided | germline | literature only | |
SCV001759994 | Genomics England Pilot Project, Genomics England | criteria provided, single submitter (ACGS Guidelines, 2016) | Likely pathogenic | germline | clinical testing | |
SCV002011971 | 3billion | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Oct 2, 2021) | germline | clinical testing | |
SCV002024864 | Revvity Omics, Revvity | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Apr 6, 2021) | germline | clinical testing | |
SCV002102990 | Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Feb 18, 2021) | de novo | clinical testing | |
SCV002507036 | Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (May 4, 2022) | germline | curation | |
SCV002512384 | Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Nov 30, 2021) | germline | clinical testing | |
SCV002757783 | Centre for Inherited Metabolic Diseases, Karolinska University Hospital | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic | de novo | clinical testing | |
SCV003918999 | Duke University Health System Sequencing Clinic, Duke University Health System | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Apr 20, 2023) | de novo | research | |
SCV004810050 | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Apr 4, 2024) | germline | clinical testing |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | de novo | yes | 2 | not provided | not provided | 1 | not provided | clinical testing, research |
not provided | germline | yes | 1 | not provided | not provided | 1 | not provided | clinical testing |
not provided | germline | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing, literature only, curation |
not provided | unknown | yes | not provided | not provided | not provided | not provided | no | clinical testing, research |
not provided | unknown | not provided | not provided | not provided | not provided | not provided | not provided | literature only |
Citations
PubMed
Mutations in G protein β subunits promote transformation and kinase inhibitor resistance.
Yoda A, Adelmant G, Tamburini J, Chapuy B, Shindoh N, Yoda Y, Weigert O, Kopp N, Wu SC, Kim SS, Liu H, Tivey T, Christie AL, Elpek KG, Card J, Gritsman K, Gotlib J, Deininger MW, Makishima H, Turley SJ, Javidi-Sharifi N, Maciejewski JP, et al.
Nat Med. 2015 Jan;21(1):71-5. doi: 10.1038/nm.3751. Epub 2014 Dec 8.
- PMID:
- 25485910
- PMCID:
- PMC4289115
Fung JLF, Yu MHC, Huang S, Chung CCY, Chan MCY, Pajusalu S, Mak CCY, Hui VCC, Tsang MHY, Yeung KS, Lek M, Chung BHY.
NPJ Genom Med. 2020;5(1):37. doi: 10.1038/s41525-020-00144-x.
- PMID:
- 32963807
- PMCID:
- PMC7484757
Details of each submission
From OMIM, SCV000282059.4
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature only | PubMed (3) |
Description
In 3 unrelated patients with autosomal dominant intellectual developmental disorder-42 (MRD42; 616973), Petrovski et al. (2016) identified a de novo heterozygous c.239T-C transition (c.239T-C, NM_002074.4) in exon 6 of the GNB1 gene, resulting in an ile80-to-thr (I80T) substitution. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was filtered against the Exome Sequencing Project (March 2013) and ExAC (January 2015) databases. The substitution occurs along the GNB1 protein surface that interacts with G-alpha subunits and downstream effectors. Yoda et al. (2015) had identified somatic I80T variants in association with hematologic transformation, including myelodysplastic syndrome (MDS; 614286) and chronic lymphocytic leukemia (CLL; 151400). I80T was demonstrated to have reduced binding to almost all G-alpha subunits, which conferred cytokine-independent growth and activation of canonical G protein downstream signaling through disruption of the G-alpha/G-beta/G-gamma interaction interface. Petrovski et al. (2016) noted that I80T has been reported in the ExAC browser as a low-confidence variant, but suggested that it may be a technical artifact or a postzygotic mutation. Functional studies of the variant and studies of patient cells were not performed by Petrovski et al. (2016). See 139380.0003 for another mutation affecting this residue.
Hemati et al. (2018) identified de novo heterozygosity for the I80T mutation in the GNB1 gene in 8 patients with MRD42.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV001150119.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | de novo | yes | 1 | blood | not provided | 1 | not provided | not provided | not provided |
From Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, SCV001364389.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | no | research | PubMed (2) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | Blood | not provided | not provided | not provided | not provided | not provided |
From Clinical Genomics Program, Stanford Medicine, SCV001427084.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | clinical testing | not provided |
Description
The p.Ile80Thr variant in the GNB1 gene has been previously reported de novo in 11 individuals with features including global developmental delay, hypotonia, seizures, and additional variable features (Hemati et al., 2018; Petrovski et al., 2016). This variant was absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). The p.Ile80Thr variant is located in a mutational hotspot of GNB1; other pathogenic and likely pathogenic variants have been described at amino acid positions 76-80 and disrupt the binding of GNB1 to other subunits. The GNB1 gene has fewer missense variants in the general population than expected. A low rate of missense variation may suggest that this gene is intolerant to missense variation. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the p.Ile80Thr variant as pathogenic for autosomal dominant GNB1-associated neurodevelopmental disorder, based on the information above. [ACMG evidence codes used: PS2_VeryStrong; PM1; PM2; PP2]
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Human Genetics, University of Leipzig Medical Center, SCV001440423.4
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
Criteria applied: PS2_VSTR,PS4,PM5_STR,PM1,PM2_SUP
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From GeneReviews, SCV001478316.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature only | PubMed (4) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Genomics England Pilot Project, Genomics England, SCV001759994.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From 3billion, SCV002011971.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (4) |
Description
Same nucleotide change resulting in same amino acid change has been previously reported as de novoo and observed in at least two similarly affected unrelated individuals (PMID: 31735425, 30194818, 27108799, PS2 and PS4). The missense variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported (PM1). It is not observed in the gnomAD v2.1.1 dataset (PM2). A different missense change ( p.Ile80Asn) at the same codon has been reported as pathogenic (PMID: 27108799, PM5). The variant was observed as assumed (i.e. paternity and maternity not confirmed) de novoo (3billion dataset, PM6). Missense changes are a common disease-causing mechanism (PP2). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided |
From Revvity Omics, Revvity, SCV002024864.3
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn, SCV002102990.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
PS1, PS2, PS3_supporting, PM1, PM2, PP2
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | de novo | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV002507036.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | curation | PubMed (1) |
Description
The heterozygous p.Ile80Thr variant in GNB1 was identified by our study in 1 individual with intellectual disability, autosomal dominant 42. Trio exome analysis showed this variant to be de novo. This variant is assumed de novo in 1 individual, but maternity and paternity have not been confirmed (PMID: 31735425). The variant has been reported in at least 15 individuals of Japanese, North African, European non-Finnish, and unknown ethnicity with intellectual disability, autosomal dominant 42 (PMID: 25485910, 27108799, 30194818, 31735425), but was absent from large population studies. This variant has also been reported in ClinVar (Variation ID: 208722) and has been interpreted as pathogenic by many labs, and likely pathogenic by University of Washington Center for Mendelian Genomics. In vitro functional studies provide some evidence that the variant may slightly impact protein function (PMID: 25485910). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. Multiple variants in the same region as p.Ile80Thr have been reported in association with disease in ClinVar and the literature and it is located in a region of GNB1 that is essential to protein folding and stability, suggesting that this variant is in a hot spot and functional domain and supports pathogenicity (PMID: 27108799). One additional likely pathogenic variant, resulting in a different amino acid change at the same position, p.Ile80Asn, has been reported in association with disease in the literature and in ClinVar, slightly supporting that a change at this position may not be tolerated (PMID: 27108799/Variation ID: 224715). The number of missense variants reported in GNB1 in the general population is lower than expected, suggesting there is little benign variation in this gene and slightly increasing the possibility that a missense variant in this gene may not be tolerated. In summary, this variant meets criteria to be classified as pathogenic for intellectual disability, autosomal dominant 42 in an autosomal dominant manner based on reports of de novo cases, absence from control databases, multiple reports of affected individuals with the variant in the literature. ACMG/AMP Criteria applied: PS2, PM2, PS4_moderate, PS3_supporting, PM1, PM5_supporting, PP2 (Richards 2015).
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein, SCV002512384.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
ACMG classification criteria: PS3 supporting, PS4 strong, PM2 moderate, PM6 strong, PP2 supporting
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Centre for Inherited Metabolic Diseases, Karolinska University Hospital, SCV002757783.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | 1 | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | de novo | yes | not provided | not provided | not provided | 1 | not provided | not provided | not provided |
From Duke University Health System Sequencing Clinic, Duke University Health System, SCV003918999.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | research | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | de novo | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004810050.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
Last Updated: May 12, 2024