ClinVar Genomic variation as it relates to human health
NM_000516.7(GNAS):c.34C>T (p.Gln12Ter)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000516.7(GNAS):c.34C>T (p.Gln12Ter)
Variation ID: 209158 Accession: VCV000209158.10
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 20q13.32 20: 58891760 (GRCh38) [ NCBI UCSC ] 20: 57466815 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Sep 29, 2015 Nov 24, 2024 Sep 20, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000516.7:c.34C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000507.1:p.Gln12Ter nonsense NM_016592.5:c.*43-3852C>T MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
intron variant NM_080425.4:c.2069-3852C>T MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
intron variant NM_000516.5:c.34C>T NM_001077488.5:c.34C>T NP_001070956.1:p.Gln12Ter nonsense NM_001077489.4:c.34C>T NP_001070957.1:p.Gln12Ter nonsense NM_001077490.3:c.*1-3852C>T intron variant NM_001309840.2:c.-39+2407C>T intron variant NM_001309842.2:c.34C>T NP_001296771.1:p.Gln12Ter nonsense NM_001309861.2:c.-38-3852C>T intron variant NM_001309883.1:c.*159-3852C>T intron variant NM_080426.4:c.34C>T NP_536351.1:p.Gln12Ter nonsense NC_000020.11:g.58891760C>T NC_000020.10:g.57466815C>T NG_016194.2:g.57021C>T - Protein change
- Q12*
- Other names
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- Canonical SPDI
- NC_000020.11:58891759:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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GNAS | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
960 | 1117 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (1) |
criteria provided, single submitter
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Oct 7, 2014 | RCV000191090.1 | |
Pathogenic (1) |
criteria provided, single submitter
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Mar 22, 2018 | RCV001265981.2 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Apr 6, 2022 | RCV002051824.2 | |
Pathogenic (1) |
criteria provided, single submitter
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Sep 11, 2021 | RCV002503750.1 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jul 13, 2024 | RCV003556238.3 | |
GNAS-related disorder
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Pathogenic (1) |
criteria provided, single submitter
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Feb 3, 2023 | RCV004530088.1 |
Pathogenic (1) |
criteria provided, single submitter
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Sep 20, 2024 | RCV004786518.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Oct 07, 2014)
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criteria provided, single submitter
Method: clinical testing
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Pseudohypoparathyroidism type 1A
Pseudopseudohypoparathyroidism (Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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Baylor Genetics
Study: Adult_WES
Accession: SCV000245487.1 First in ClinVar: Sep 29, 2015 Last updated: Sep 29, 2015 |
Comment:
This variant has been previously reported as disease-causing and was found once in our laboratory de novo in a 21-year-old female with IUGR, mild motor … (more)
This variant has been previously reported as disease-causing and was found once in our laboratory de novo in a 21-year-old female with IUGR, mild motor delay, intellectual disability, hearing loss, mild Tourette/tics, short stature, and irregular phalanges. (less)
Number of individuals with the variant: 2
Zygosity: Homozygote, Single Heterozygote, Compound Heterozygote
Age: 1-21 years
Sex: mixed
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Pathogenic
(Mar 22, 2022)
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criteria provided, single submitter
Method: clinical testing
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Pseudopseudohypoparathyroidism
Affected status: yes
Allele origin:
germline
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3billion
Accession: SCV002318828.1
First in ClinVar: Apr 02, 2022 Last updated: Apr 02, 2022 |
Comment:
Stop-gained (nonsense): predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are … (more)
Stop-gained (nonsense): predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant.It is not observed in the gnomAD v2.1.1 dataset. The variant has been reported at least twice as pathogenic/likely pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000209158, PMID:11092390). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Brachydactyly (present) , Congenital hypothyroidism (present) , Seizure (present) , Hypocalcemia (present) , Intellectual disability (present) , Obesity (present) , Round face (present) , Short … (more)
Brachydactyly (present) , Congenital hypothyroidism (present) , Seizure (present) , Hypocalcemia (present) , Intellectual disability (present) , Obesity (present) , Round face (present) , Short stature (present) , Short metacarpal (present) (less)
Zygosity: Single Heterozygote
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Pathogenic
(Mar 22, 2018)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: yes
Allele origin:
germline
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Ambry Genetics
Accession: SCV001444153.2
First in ClinVar: Nov 21, 2020 Last updated: Jan 07, 2023 |
Number of individuals with the variant: 1
Clinical Features:
Obstructive sleep apnea syndrome (present) , Hypothyroidism (present) , Obesity (present) , Hypertelorism (present) , Short stature (present) , Polycystic ovaries (present) , Upslanted palpebral … (more)
Obstructive sleep apnea syndrome (present) , Hypothyroidism (present) , Obesity (present) , Hypertelorism (present) , Short stature (present) , Polycystic ovaries (present) , Upslanted palpebral fissure (present) , Delayed speech and language development (present) , Brachymetatarsus 4 (present) , Short 4th finger (present) (less)
Sex: female
Ethnicity/Population group: Hispanic/Mexican
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Pathogenic
(Apr 06, 2022)
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criteria provided, single submitter
Method: clinical testing
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Pseudopseudohypoparathyroidism
Affected status: unknown
Allele origin:
germline
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Johns Hopkins Genomics, Johns Hopkins University
Accession: SCV002570266.1
First in ClinVar: Sep 17, 2022 Last updated: Sep 17, 2022 |
Comment:
This GNAS variant has been identified in multiple individuals with a clinical presentation consistent with a GNAS-related condition. It is absent from a large population … (more)
This GNAS variant has been identified in multiple individuals with a clinical presentation consistent with a GNAS-related condition. It is absent from a large population dataset, and has been reported in ClinVar (Variation ID 209158). This nonsense variant results in a premature stop codon in exon 1 likely leading to nonsense-mediated decay and lack of protein production. We consider this variant to be pathogenic. (less)
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Pathogenic
(Sep 11, 2021)
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criteria provided, single submitter
Method: clinical testing
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Pseudohypoparathyroidism type I A
Progressive osseous heteroplasia McCune-Albright syndrome ACTH-independent macronodular adrenal hyperplasia 1 Pseudohypoparathyroidism type 1B Pseudohypoparathyroidism type 1C Pseudopseudohypoparathyroidism Pituitary adenoma 3, multiple types
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002796490.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Pathogenic
(Feb 03, 2023)
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criteria provided, single submitter
Method: clinical testing
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GNAS-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004115020.1
First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023 |
Comment:
The GNAS c.34C>T variant is predicted to result in premature protein termination (p.Gln12*). This variant has been reported in many individuals to be pathogenic for … (more)
The GNAS c.34C>T variant is predicted to result in premature protein termination (p.Gln12*). This variant has been reported in many individuals to be pathogenic for pseudohypoparathyroidism (PHP) or progressive osseous heteroplasia (POH); it was reported to have occurred de novo in multiple patients (Richard et al. 2013. PubMed ID: 23884777; Eddy et al. 2000. PubMed ID: 11092390; Salemi P et al 2018. PubMed ID: 29059381). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating it is rare. Nonsense variants in GNAS are expected to be pathogenic. In summary, this variant is interpreted as pathogenic GNAS-related disorders. (less)
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Pathogenic
(May 16, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV004298102.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 209158). This premature translational stop signal … (more)
For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 209158). This premature translational stop signal has been observed in individual(s) with GNAS-related conditions (PMID: 11092390, 21525160, 23533243, 27703483, 29059381, 31886927, 33144682). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln12*) in the GNAS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GNAS are known to be pathogenic (PMID: 11784876, 23281139, 23796510, 25802881). (less)
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Pathogenic
(Jul 13, 2024)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV005078106.1
First in ClinVar: Jul 23, 2024 Last updated: Jul 23, 2024 |
Comment:
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of … (more)
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 21525160, 11092390, 23533243, 27703483, 31886927, 33144682, 29059381) (less)
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Pathogenic
(Sep 20, 2024)
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criteria provided, single submitter
Method: clinical testing
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Pseudohypoparathyroidism type I A
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV005400329.1
First in ClinVar: Nov 24, 2024 Last updated: Nov 24, 2024 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Both loss- and gain-of-function are known mechanisms … (more)
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Both loss- and gain-of-function are known mechanisms of disease for this gene. Loss-of-function has been associated with the hypoparathyroidism phenotypes (PMID: 10980525), while gain-of-function has been reported for somatic variants in cancers (PMID: 11588148). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0113 - This gene is known to be imprinted and the imprinting can be transcript dependent (OMIM, PMID: 23884777). (I) 0115 - Variants in this gene are known to have variable expressivity (PMID: 29072892). (I) 0204 - Variant is predicted to result in a truncated protein (premature termination codon is located within the first 102 nucleotides of the coding sequence and is predicted to escape nonsense-mediated decay). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0701 - Other premature termination codon variants within the first 102 nucleotides comparable to the one identified in this case have very strong previous evidence for pathogenicity (DECIPHER, PMID: 17164301). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic by multiple clinical laboratories in ClinVar, and has been observed in individuals with pseudohypoparathyroidism Ia and pseudopseudohypoparathyroidism (PMID: 29059381, 29379892). (SP) 1203 - This variant has been shown to be de novo in the proband (parental status confirmed) (by trio analysis). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Impact of integrated translational research on clinical exome sequencing. | Klee EW | Genetics in medicine : official journal of the American College of Medical Genetics | 2021 | PMID: 33144682 |
Maternal Transmission Ratio Distortion of GNAS Loss-of-Function Mutations. | Snanoudj S | Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research | 2020 | PMID: 31886927 |
Ossifications in Albright Hereditary Osteodystrophy: Role of Genotype, Inheritance, Sex, Age, Hormonal Status, and BMI. | Salemi P | The Journal of clinical endocrinology and metabolism | 2018 | PMID: 29059381 |
(Epi)genotype-Phenotype Analysis in 69 Japanese Patients With Pseudohypoparathyroidism Type I. | Sano S | Journal of the Endocrine Society | 2017 | PMID: 29379892 |
Disorders of GNAS Inactivation. | Adam MP | - | 2017 | PMID: 29072892 |
The Association of Pseudohypoparathyroidism Type Ia with Chiari Malformation Type I: A Coincidence or a Common Link? | Kashani P | Case reports in medicine | 2016 | PMID: 27703483 |
Molecular diagnostic experience of whole-exome sequencing in adult patients. | Posey JE | Genetics in medicine : official journal of the American College of Medical Genetics | 2016 | PMID: 26633545 |
A positive genotype-phenotype correlation in a large cohort of patients with Pseudohypoparathyroidism Type Ia and Pseudo-pseudohypoparathyroidism and 33 newly identified mutations in the GNAS gene. | Thiele S | Molecular genetics & genomic medicine | 2015 | PMID: 25802881 |
Paternal GNAS mutations lead to severe intrauterine growth retardation (IUGR) and provide evidence for a role of XLαs in fetal development. | Richard N | The Journal of clinical endocrinology and metabolism | 2013 | PMID: 23884777 |
Screening for GNAS genetic and epigenetic alterations in progressive osseous heteroplasia: first Italian series. | Elli FM | Bone | 2013 | PMID: 23796510 |
Endocrine profile and phenotype-(epi)genotype correlation in Spanish patients with pseudohypoparathyroidism. | Fernández-Rebollo E | The Journal of clinical endocrinology and metabolism | 2013 | PMID: 23533243 |
Pseudohypoparathyroidism type Ia and pseudo-pseudohypoparathyroidism: the growing spectrum of GNAS inactivating mutations. | Elli FM | Human mutation | 2013 | PMID: 23281139 |
Increased prevalence of carpal tunnel syndrome in albright hereditary osteodystrophy. | Joseph AW | The Journal of clinical endocrinology and metabolism | 2011 | PMID: 21525160 |
Body mass index differences in pseudohypoparathyroidism type 1a versus pseudopseudohypoparathyroidism may implicate paternal imprinting of Galpha(s) in the development of human obesity. | Long DN | The Journal of clinical endocrinology and metabolism | 2007 | PMID: 17164301 |
Paternally inherited inactivating mutations of the GNAS1 gene in progressive osseous heteroplasia. | Shore EM | The New England journal of medicine | 2002 | PMID: 11784876 |
Endocrine manifestations of stimulatory G protein alpha-subunit mutations and the role of genomic imprinting. | Weinstein LS | Endocrine reviews | 2001 | PMID: 11588148 |
Deficiency of the alpha-subunit of the stimulatory G protein and severe extraskeletal ossification. | Eddy MC | Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research | 2000 | PMID: 11092390 |
Activating and inactivating mutations in the human GNAS1 gene. | Aldred MA | Human mutation | 2000 | PMID: 10980525 |
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Text-mined citations for rs797045046 ...
HelpRecord last updated Jan 13, 2025
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.