U.S. flag

An official website of the United States government

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 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no 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
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)

Name:
Intellectual disability, autosomal dominant 42 (MRD42)
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 42
Identifiers:
MONDO: MONDO:0014855; MedGen: C4310774; OMIM: 616973

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000282059OMIM
no assertion criteria provided
Pathogenic
(Nov 2, 2021)
unknownliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV001150119Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
criteria provided, single submitter

(Classification criteria August 2017)
Pathogenic
(Aug 19, 2019)
de novoclinical testing

Citation Link,

SCV001364389Department of Paediatrics and Adolescent Medicine, The University of Hong Kong
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 2, 2020)
unknownresearch

PubMed (2)
[See all records that cite these PMIDs]

SCV001427084Clinical Genomics Program, Stanford Medicine
no assertion criteria provided
Pathogenic
(Sep 26, 2019)
germlineclinical testing

SCV001440423Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 20, 2024)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001478316GeneReviews
no classification provided
not providedgermlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV001759994Genomics England Pilot Project, Genomics England
criteria provided, single submitter

(ACGS Guidelines, 2016)
Likely pathogenicgermlineclinical testing

Citation Link,

SCV0020119713billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 2, 2021)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV002024864Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 6, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002102990Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 18, 2021)
de novoclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002507036Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 4, 2022)
germlinecuration

PubMed (1)
[See all records that cite this PMID]

SCV002512384Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Nov 30, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002757783Centre for Inherited Metabolic Diseases, Karolinska University Hospital
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicde novoclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV003918999Duke University Health System Sequencing Clinic, Duke University Health System
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 20, 2023)
de novoresearch

PubMed (1)
[See all records that cite this PMID]

SCV004810050Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 4, 2024)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes2not providednot provided1not providedclinical testing, research
not providedgermlineyes1not providednot provided1not providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, literature only, curation
not providedunknownyesnot providednot providednot providednot providednoclinical testing, research
not providedunknownnot providednot providednot providednot providednot providednot providedliterature 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.

PubMed [citation]
PMID:
25485910
PMCID:
PMC4289115

A three-year follow-up study evaluating clinical utility of exome sequencing and diagnostic potential of reanalysis.

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.

PubMed [citation]
PMID:
32963807
PMCID:
PMC7484757
See all PubMed Citations (7)

Details of each submission

From OMIM, SCV000282059.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownnot providednot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV001150119.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyes1bloodnot provided1not providednot providednot provided

From Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, SCV001364389.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednoresearch PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providedBloodnot providednot providednot providednot providednot provided

From Clinical Genomics Program, Stanford Medicine, SCV001427084.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testingnot 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]

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001440423.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Criteria applied: PS2_VSTR,PS4,PM5_STR,PM1,PM2_SUP

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From GeneReviews, SCV001478316.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Genomics England Pilot Project, Genomics England, SCV001759994.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From 3billion, SCV002011971.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

From Revvity Omics, Revvity, SCV002024864.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn, SCV002102990.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

PS1, PS2, PS3_supporting, PM1, PM2, PP2

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot providednot providednot providednot providednot provided

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV002507036.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration 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).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein, SCV002512384.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

ACMG classification criteria: PS3 supporting, PS4 strong, PM2 moderate, PM6 strong, PP2 supporting

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Centre for Inherited Metabolic Diseases, Karolinska University Hospital, SCV002757783.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot provided1not providednot providednot provided

From Duke University Health System Sequencing Clinic, Duke University Health System, SCV003918999.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot providednot providednot providednot providednot provided

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004810050.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 12, 2024