ClinVar Genomic variation as it relates to human health
NM_000823.4(GHRHR):c.57+1G>A
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_000823.4(GHRHR):c.57+1G>A
Variation ID: 15990 Accession: VCV000015990.8
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 7p14.3 7: 30964126 (GRCh38) [ NCBI UCSC ] 7: 31003741 (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 Nov 3, 2018 Sep 16, 2024 Jul 2, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000823.4:c.57+1G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
splice donor NC_000007.14:g.30964126G>A NC_000007.13:g.31003741G>A NG_021416.1:g.5106G>A - Protein change
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- Other names
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IVS1, G-A, +1
- Canonical SPDI
- NC_000007.14:30964125:G:A
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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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The Genome Aggregation Database (gnomAD), exomes 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00005
The Genome Aggregation Database (gnomAD) 0.00007
- Links
- Comment on variant
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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GHRHR | - | - |
GRCh38 GRCh37 |
260 | 292 |
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) |
no assertion criteria provided
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Dec 1, 2007 | RCV000017361.28 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jul 2, 2024 | RCV001568303.7 |
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
Help
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
(Jul 02, 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: SCV001792146.2
First in ClinVar: Aug 19, 2021 Last updated: Sep 16, 2024 |
Comment:
Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; … (more)
Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 28456063, 31902114, 32935264, 23052699, 24057284, 24398366, 10084571, 25761575, 27552668, 24272598, 30959475, 29571594, 30860584, 31980526, 28428227, 28432269, 11443201, 16522693, 16355809, 10822217) (less)
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Pathogenic
(Dec 19, 2021)
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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: SCV003285506.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 14, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this … (more)
For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 15990). Disruption of this splice site has been observed in individuals with growth hormone deficiency (PMID: 10084571, 23052699). It has also been observed to segregate with disease in related individuals. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change affects a donor splice site in intron 1 of the GHRHR gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in GHRHR are known to be pathogenic (PMID: 12444890, 16355809). (less)
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Pathogenic
(Dec 01, 2007)
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no assertion criteria provided
Method: literature only
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ISOLATED GROWTH HORMONE DEFICIENCY, TYPE IV
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000037633.2
First in ClinVar: Apr 04, 2013 Last updated: Nov 03, 2018 |
Comment on evidence:
Salvatori et al. (1999) examined 22 affected members of a large extended Brazilian kindred (Itabaianinha cohort) containing at least 105 members with autosomal recessive short … (more)
Salvatori et al. (1999) examined 22 affected members of a large extended Brazilian kindred (Itabaianinha cohort) containing at least 105 members with autosomal recessive short stature (IGHD4; 618157), formerly IGHD1B, Extensive endocrine evaluation confirmed markedly reduced or undetectable serum concentrations of GH that did not increase in response to different stimuli. Analysis of the GHRHR gene detected a novel homozygous 5-prime splice site mutation, a G-to-A transition at position +1 of intron 1. Thirty of the affected subjects tested were homozygous for this mutation, and of 64 clinically unaffected patients, 41, including 9 obligate carriers, were heterozygous for the mutation and 23 were homozygous for the wildtype sequence. Aguiar-Oliveira et al. (1999) measured insulin-like growth factor I (IGF1; 147440), IGF2 (147470), IGF-binding protein-1 (IGFBP1; 146730), IGFBP2 (146731), IGFBP3 (146732), and acid labile subunit (ALS; 601489) in 27 subjects with GHD (aged 5 to 82 years) from the Itabaianinha cohort with the intron 1 splice site GHRHR mutation and in 55 indigenous controls (aged 5 to 80 years). All components of the IGF axis, measured and theoretical, showed complete separation between GHD and control subjects, except IGFBP1 and IGFBP2 concentrations, which did not differ. The most profound effects of GHD were on total IGF1, IGF1 in the ternary complex, and ALS. The proportion of IGF1 associated with IGFBP3 remained constant throughout life, but was significantly lower in GHD due to an increase in IGF1/IGFBP2 complexes. As diagnostic tests, IGF1 in the ternary complex and total IGF1 provided the greatest separation between GHD and controls in childhood. The authors concluded that severe GHD not only reduces the amounts of IGFs, IGFBP3, and ALS, but also modifies the distribution of the IGFs bound to each IGFBP. Diagnostic tests used in the investigation of GHD should be tailored to the age of the individual. In particular, measurement of IGF1 in the ternary complex may prove useful in the diagnosis of GHD in children and older adults, whereas free ALS may be more relevant to younger adults. Gondo et al. (2001) compared the pituitary hormone response to GHRP-2, a potent growth hormone secretagogue, in 11 affected individuals from the Itabaianinha cohort with this mutation and in 8 normal unrelated controls. Basal serum GH levels were lower in the GHD group compared with controls. After GHRP-2 administration, there was a 4.5-fold increase in serum GH relative to baseline values in the GHD group, which was significantly less than the 79-fold increase in the control group. The authors concluded that an intact GHRH signaling system is not an absolute requirement for GHRP-2 action on GH secretion and that GHRP-2 has a GHRH-independent effect on pituitary somatotroph cells. Menezes Oliveira et al. (2006) studied the consequences of lifetime IGHD on the metabolic and cardiovascular status of adult members of the large Brazilian kindred (Itabaianinha cohort) with severe IGHD reported by Salvatori et al. (1999). GHD subjects had increased abdominal obesity, higher total and low density lipoprotein cholesterol, and higher C-reactive protein (123260) than controls. They did not have an increase in carotid wall thickness, and there was no evidence of premature atherosclerosis as evaluated by exercise echocardiography. The authors concluded that in this homogeneous cohort, untreated severe IGHD is not associated with evidence of premature atherosclerosis despite unfavorable cardiovascular risk profile. Pereira et al. (2007) compared 76 adult subjects (age, 25-75 years) from the Itabaianinha cohort who were heterozygous for the IVS1+1G-A mutation with 77 sex-matched controls from the same population who were homozygous for the wildtype GHRHR allele. They found no difference in adult height or SD score for serum IGF-I between the 2 groups. However, body weight, body mass index, skin folds, waist and hip circumferences, and lean mass were all reduced in heterozygous subjects. The authors concluded that heterozygosity for a null GHRHR mutation is associated with changes in body composition and possibly an increase in insulin sensitivity. Oliveira et al. (2007) reported that in patients with lifetime isolated GHD due to IVS1+1G-A homozygosity, 6-month treatment with GH had reversible beneficial effects on body composition and metabolic profile, but caused a progressive increase in intima-media thickness and in the number of atherosclerotic carotid plaques. (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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GH-releasing hormone receptor gene: a novel splice-disrupting mutation and study of founder effects. | Marui S | Hormone research in paediatrics | 2012 | PMID: 23052699 |
Congenital growth hormone (GH) deficiency and atherosclerosis: effects of GH replacement in GH-naive adults. | Oliveira JL | The Journal of clinical endocrinology and metabolism | 2007 | PMID: 17911170 |
Heterozygosity for a mutation in the growth hormone-releasing hormone receptor gene does not influence adult stature, but affects body composition. | Pereira RM | The Journal of clinical endocrinology and metabolism | 2007 | PMID: 17356054 |
Lack of evidence of premature atherosclerosis in untreated severe isolated growth hormone (GH) deficiency due to a GH-releasing hormone receptor mutation. | Menezes Oliveira JL | The Journal of clinical endocrinology and metabolism | 2006 | PMID: 16522693 |
Growth hormone releasing hormone receptor (GHRH-r) gene mutation in Indian children with familial isolated growth hormone deficiency: a study from western India. | Desai MP | Journal of pediatric endocrinology & metabolism : JPEM | 2005 | PMID: 16355809 |
Splicing in action: assessing disease causing sequence changes. | Baralle D | Journal of medical genetics | 2005 | PMID: 16199547 |
Serum GH response to pharmacological stimuli and physical exercise in two siblings with two new inactivating mutations in the GH-releasing hormone receptor gene. | Salvatori R | European journal of endocrinology | 2002 | PMID: 12444890 |
Growth hormone-releasing peptide-2 stimulates GH secretion in GH-deficient patients with mutated GH-releasing hormone receptor. | Gondo RG | The Journal of clinical endocrinology and metabolism | 2001 | PMID: 11443201 |
Effect of severe growth hormone (GH) deficiency due to a mutation in the GH-releasing hormone receptor on insulin-like growth factors (IGFs), IGF-binding proteins, and ternary complex formation throughout life. | Aguiar-Oliveira MH | The Journal of clinical endocrinology and metabolism | 1999 | PMID: 10566659 |
Familial dwarfism due to a novel mutation of the growth hormone-releasing hormone receptor gene. | Salvatori R | The Journal of clinical endocrinology and metabolism | 1999 | PMID: 10084571 |
Text-mined citations for rs2302022 ...
HelpRecord last updated Sep 29, 2024
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.
ClinGen staff contributed the HGVS expression for this variant.