GNAS
protein-codingGNAS complex locus, the group of Granins|G protein subunits alpha, group s
Gene summary
This locus has a highly complex imprinted expression pattern. It gives rise to maternally, paternally, and biallelically expressed transcripts that are derived from four alternative promoters and 5' exons. Some transcripts contain a differentially methylated region (DMR) at their 5' exons, and this DMR is commonly found in imprinted genes and correlates with transcript expression. An antisense transcript is produced from an overlapping locus on the opposite strand. One of the transcripts produced from this locus, and the antisense transcript, are paternally expressed noncoding RNAs, and may regulate imprinting in this region. In addition, one of the transcripts contains a second overlapping ORF, which encodes a structurally unrelated protein - Alex. Alternative splicing of downstream exons is also observed, which results in different forms of the stimulatory G-protein alpha subunit, a key element of the classical signal transduction pathway linking receptor-ligand interactions with the activation of adenylyl cyclase and a variety of cellular reponses. Multiple transcript variants encoding different isoforms have been found for this gene. Mutations in this gene result in pseudohypoparathyroidism type 1a, pseudohypoparathyroidism type 1b, Albright hereditary osteodystrophy, pseudopseudohypoparathyroidism, McCune-Albright syndrome, progressive osseus heteroplasia, polyostotic fibrous dysplasia of bone, and some pituitary tumors. [provided by RefSeq, Aug 2012]
- GNAS1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~71.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0011301
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0018919
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0011301
Submitter: Orphanet
Inheritance Pattern: Unknown
Disease ID:MONDO:0018919
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0008153
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0012911
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0012911
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007078
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007078
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0012912
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0008153
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0008153
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0012912
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007078
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0007078
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0018919
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0800466
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0019992
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0012912
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0008153
Submitter: G2P
Inheritance Pattern: Unknown
Disease ID:MONDO:0018919
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Dermatologic; Endocrine; Musculoskeletal; Oncologic; Renal
Intervention: Endocrine; Oncologic; Renal
Rationale: In Pseudohypoparathyroidism, medical treatment (eg, with calcium and vitamin D therapy) of electrolyte abnormalities and related complications such as osteitis fibrosa cystica can be effective, and complications; Surveillance and early treatment of endocrinological manifestations (eg, hypothyroidism, hypogonadism) can be beneficial; In McCune-Albright syndrome, medical (eg, related to estrogen production, hyperthyroidism, growth hormone production) and surgical (eg, to treat adrenal pathology, hyperthyroidism) treatment of endocrinopathies may be beneficial, and surveillance and early and specific treatment for manifestations such as a number of types of neoplasms, including GH-producing tumors (eg, with long-acting octreotide, GHR antagonists) can be beneficial, as well as surveillance for and treatment of Cushing syndrome (some patients require adrenalectomy)
Comments: Mosaic variants have been described; PPHP occurs with paternal inheritance
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GNAS variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000516.7. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 11 | 134 | 1 | 146 | ||
| missense | 29 | 70 | 200 | 299 | ||
| nonsense | 28 | 5 | 33 | |||
| start loss | 6 | 4 | 10 | |||
| frameshift | 47 | 21 | 1 | 69 | ||
| splice donor/acceptor (+/-2bp) | 26 | 17 | 11 | 54 | ||
| Total | 136 | 117 | 223 | 134 | 1 | 611 |
Highest pathogenic variant AF is 0.000024797006
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000507.1 | 13 | MANE Select | |
| Ensembl | ENSP00000360126.3 | 13 | MANE Select | |
| RefSeq | NP_001070956.1 | 13 | Standard | |
| RefSeq | NP_001070957.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Inflammatory mediator regulation of TRP channels - Homo sapiens (human)
- Platelet activation - Homo sapiens (human)
- Cortisol synthesis and secretion - Homo sapiens (human)
- Relaxin signaling pathway - Homo sapiens (human)
- Aldosterone synthesis and secretion - Homo sapiens (human)
Biological Process
- tissue homeostasis
- endochondral ossification
- energy reserve metabolic process
- DNA methylation
- adenylate cyclase-modulating G protein-coupled receptor signaling pathway
Molecular Function
- G protein-coupled receptor binding
- GTPase activity
- insulin-like growth factor receptor binding
- protein binding
- GTP binding
Cellular Component
- cytosol
- heterotrimeric G-protein complex
- membrane
- apical plasma membrane
- dendrite
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000371100
- Coding exons
- 13
- Length
- 71475
- Individuals with no LoFs
- 124575
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 38
- Defined
- 124614
- p
- 0.000157
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.65 | 460 | 651 | 0.707 | 0.0000436 | 6674 |
| Missense (PolyPhen) | 42 | 196.77 | 0.21345 | 2112 | ||
| Synonymous | -0.174 | 275 | 271 | 1.01 | 0.0000211 | 2131 |
| Loss of Function | 4.59 | 8 | 38.9 | 0.206 | 0.00000209 | 426 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000067 | 0.000065 | rare |
| Latino/Admixed American | 0.000091 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00026 | 0.00024 | rare |
| South Asian | 0.00017 | 0.00013 | rare |
| Other | 0.00017 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Disease
- DISEASE: ACTH-independent macronodular adrenal hyperplasia 1 (AIMAH1) [MIM:219080]: A rare adrenal defect characterized by multiple, bilateral, non-pigmented, benign, adrenocortical nodules. It results in excessive production of cortisol leading to ACTH-independent Cushing syndrome. Clinical manifestations of Cushing syndrome include facial and truncal obesity, abdominal striae, muscular weakness, osteoporosis, arterial hypertension, diabetes. {ECO:0000269|PubMed:12727968}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Pseudohypoparathyroidism 1B (PHP1B) [MIM:603233]: A disorder characterized by end-organ resistance to parathyroid hormone, hypocalcemia and hyperphosphatemia. Patients affected with PHP1B lack developmental defects characteristic of Albright hereditary osteodystrophy, and typically show no other endocrine abnormalities besides resistance to PTH. {ECO:0000269|PubMed:11029463, ECO:0000269|PubMed:11067869, ECO:0000269|PubMed:11294659, ECO:0000269|PubMed:12858292, ECO:0000269|PubMed:14561710, ECO:0000269|PubMed:15592469, ECO:0000269|PubMed:15800843}. Note=The disease is caused by mutations affecting the gene represented in this entry. Most affected individuals have defects in methylation of the gene. In some cases microdeletions involving the STX16 appear to cause loss of methylation at exon A/B of GNAS, resulting in PHP1B. Paternal uniparental isodisomy have also been observed.; DISEASE: GNAS hyperfunction (GNASHYP) [MIM:139320]: This condition is characterized by increased trauma-related bleeding tendency, prolonged bleeding time, brachydactyly and mental retardation. Both the XLas isoforms and the ALEX protein are mutated which strongly reduces the interaction between them and this may allow unimpeded activation of the XLas isoforms. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.800
Intolerance Scores
- LoFtool
- 0.00834
- RVIS EVS
- -0.02
- RVIS percentile EVS
- 52.32
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.387
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |