ClinVar Genomic variation as it relates to human health
NM_003001.5(SDHC):c.380A>G (p.His127Arg)
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_003001.5(SDHC):c.380A>G (p.His127Arg)
Variation ID: 187084 Accession: VCV000187084.21
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1q23.3 1: 161356815 (GRCh38) [ NCBI UCSC ] 1: 161326605 (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 Dec 19, 2017 Jun 17, 2024 Feb 8, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_003001.5:c.380A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_002992.1:p.His127Arg missense NM_001035511.3:c.242-5514A>G intron variant NM_001035512.3:c.278A>G NP_001030589.1:p.His93Arg missense NM_001035513.3:c.221A>G NP_001030590.1:p.His74Arg missense NM_001278172.3:c.140-5514A>G intron variant NM_001407115.1:c.500A>G NP_001394044.1:p.His167Arg missense NM_001407116.1:c.323A>G NP_001394045.1:p.His108Arg missense NM_001407117.1:c.317A>G NP_001394046.1:p.His106Arg missense NM_001407118.1:c.272A>G NP_001394047.1:p.His91Arg missense NM_001407119.1:c.269A>G NP_001394048.1:p.His90Arg missense NM_001407120.1:c.269A>G NP_001394049.1:p.His90Arg missense NM_001407121.1:c.185-5514A>G intron variant NR_103459.3:n.432A>G non-coding transcript variant NC_000001.11:g.161356815A>G NC_000001.10:g.161326605A>G NG_012767.1:g.47440A>G LRG_317:g.47440A>G LRG_317t1:c.380A>G LRG_317p1:p.His127Arg - Protein change
- H127R, H74R, H93R, H106R, H167R, H91R, H108R, H90R
- Other names
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- Canonical SPDI
- NC_000001.11:161356814:A:G
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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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Trans-Omics for Precision Medicine (TOPMed) 0.00000
The Genome Aggregation Database (gnomAD) 0.00001
- 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
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
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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SDHC | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
862 | 904 |
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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May 27, 2021 | RCV000166772.10 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Dec 3, 2022 | RCV000478217.7 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 16, 2024 | RCV000641906.9 | |
Pathogenic/Likely pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Dec 7, 2023 | RCV001523820.5 | |
Likely pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Oct 2, 2023 | RCV003995530.2 | |
Likely pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Feb 8, 2024 | RCV004019988.2 |
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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Likely pathogenic
(Dec 15, 2020)
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criteria provided, single submitter
Method: research
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Gastrointestinal stromal tumor
Affected status: no
Allele origin:
germline
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Department of Pediatrics, Memorial Sloan Kettering Cancer Center
Accession: SCV001478182.1
First in ClinVar: Jun 19, 2021 Last updated: Jun 19, 2021 |
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Likely pathogenic
(Dec 03, 2022)
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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: SCV000565547.5
First in ClinVar: Apr 27, 2017 Last updated: Dec 31, 2022 |
Comment:
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); … (more)
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 23162105, 29386252, 25025441, 31579262, 19332149, 23666964, 26259135, 25494863, 23282968, 25394176, 24886695, 26273102, 23833252, 24625421, 24096523, 27011036, 33087929, 34703596, 34558728, 33237286, 24150194, 34308366, 34110302, 34301805) (less)
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Pathogenic
(Jan 16, 2024)
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criteria provided, single submitter
Method: clinical testing
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Paragangliomas 3
Gastrointestinal stromal tumor
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000763556.6
First in ClinVar: May 28, 2018 Last updated: Feb 28, 2024 |
Comment:
This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 127 of the SDHC protein (p.His127Arg). … (more)
This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 127 of the SDHC protein (p.His127Arg). This variant is present in population databases (rs786203457, gnomAD no frequency). This missense change has been observed in individuals with gastrointestinal stromal tumor, renal carcinoma and papillary thyroid carcinoma and paraganglioma (PMID: 23666964, 24150194, 25494863; Invitae). ClinVar contains an entry for this variant (Variation ID: 187084). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SDHC protein function with a positive predictive value of 95%. RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). This variant disrupts the p.His127 amino acid residue in SDHC. Other variant(s) that disrupt this residue have been observed in individuals with SDHC-related conditions (PMID: 22517557, 24758179), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. (less)
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Likely Pathogenic
(Oct 02, 2023)
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criteria provided, single submitter
Method: clinical testing
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Hereditary pheochromocytoma-paraganglioma
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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All of Us Research Program, National Institutes of Health
Accession: SCV004836972.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024
Comment:
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of … (more)
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of variant classification. Additional details can be found in publication PMID: 35346344, PMCID: PMC8962531 (less)
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Comment:
This missense variant replaces histidine with arginine at codon 127 of the SDHC protein. Computational prediction suggests that this variant may have deleterious impact on … (more)
This missense variant replaces histidine with arginine at codon 127 of the SDHC protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant, however histidine-127 is a key amino acid for heme binding (PMID: 15989954) and mutations of this residue abolish SDHC protein levels, destabilize of SDHD and SDHB level, and abrogate both succinate ubiquinone oxidoreductase (SQR) and succinate dehydrogenase (SDH) (complex II) enzymatic activities in mitochondria (PMID: 19332149). This variant has been reported in individuals affected with paragangliomas, gastrointestinal stromal tumors (GIST), renal cell carcinoma, and pituitary adenomas (PMID: 23282968, 23666964, 24150194, 24625421, 25025441, 25494863, 29386252, 31308404, 34110302, 34558728). This variant has been identified in 1/31390 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. (less)
Number of individuals with the variant: 1
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Likely Pathogenic
(Aug 10, 2020)
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criteria provided, single submitter
Method: clinical testing
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Hereditary pheochromocytoma-paraganglioma
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV004847997.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024 |
Comment:
The p.His127Arg variant in SDHC has been reported in 6 individuals with SDHC-related tumors and segregated with disease in 1 affected individual from 1 family … (more)
The p.His127Arg variant in SDHC has been reported in 6 individuals with SDHC-related tumors and segregated with disease in 1 affected individual from 1 family (Gill 2013 PMID: 24150194; Miettinen 2013 PMID: 23282968; Denes 2015 PMID: 25494863; Rattenberry 2013 PMID: 23666964; Casey 2019 PMID 31308404; Invitae). It was absent from large population studies. This variant has also been reported in ClinVar (Variation ID 187084). Computational prediction tools and conservation analysis suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant SDHC-related tumors. ACMG/AMP Criteria applied: PM2, PP3, PS4_Strong. (less)
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Likely pathogenic
(Feb 08, 2024)
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criteria provided, single submitter
Method: clinical testing
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Paragangliomas 3
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV004933699.1
First in ClinVar: May 01, 2024 Last updated: May 01, 2024 |
Comment:
This variant is considered likely pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 25494863, 24150194, 23666964]. This … (more)
This variant is considered likely pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 25494863, 24150194, 23666964]. This variant is expected to disrupt protein structure [Myriad internal data]. (less)
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Pathogenic
(May 27, 2021)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000217585.8
First in ClinVar: Mar 24, 2015 Last updated: May 01, 2024 |
Comment:
The p.H127R pathogenic mutation (also known as c.380A>G), located in coding exon 5 of the SDHC gene, results from an A to G substitution at … (more)
The p.H127R pathogenic mutation (also known as c.380A>G), located in coding exon 5 of the SDHC gene, results from an A to G substitution at nucleotide position 380. The histidine at codon 127 is replaced by arginine, an amino acid with highly similar properties. The mutation has been detected in multiple individuals with paraganglioma(s) (Rattenberry E et al. J Clin Endocrinol Metab, 2013 Jul;98:E1248-56; Dénes J et al. J Clin Endocrinol Metab, 2015 Mar;100:E531-41; Andrews KA et al. J Med Genet, 2018 06;55:384-394; Ambry internal data). It has also been identified in patients with a succinate dehydrogenase (SDH)-deficient gastrointestinal stromal tumor and/or renal carcinoma (Gill AJ et al. Pathology, 2013 12;45:689-91; Gill AJ et al. Am J Surg Pathol, 2014 Dec;38:1588-602; Casey RT et al. Sci Rep, 2019 07;9:10244; Ambry internal data). Based on internal structural analysis, this mutation disrupts the SDHC heme-binding site, within which there are other internally pathogenic variants (Sun F et al. Cell, 2005 Jul;121:1043-57; Fufezan C et al. Proteins, 2008 Nov;73:690-704; Lemarie A et al. Mitochondrion, 2009 Jul;9:254-60). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. (less)
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Likely pathogenic
(Dec 12, 2023)
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criteria provided, single submitter
Method: clinical testing
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paragangliomas 3
Affected status: unknown
Allele origin:
unknown
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Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine
Accession: SCV005045796.1
First in ClinVar: Jun 02, 2024 Last updated: Jun 02, 2024 |
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Pathogenic
(Dec 07, 2023)
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criteria provided, single submitter
Method: clinical testing
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Gastrointestinal stromal tumor
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004203056.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
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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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SDHC phaeochromocytoma and paraganglioma: A UK-wide case series. | Williams ST | Clinical endocrinology | 2022 | PMID: 34558728 |
Cabergoline reduces 3-methoxytyramine in a SDHC patient with metastatic paraganglioma and prolactinoma. | Hussein Z | Endocrinology, diabetes & metabolism case reports | 2021 | PMID: 34110302 |
SDHC epi-mutation testing in gastrointestinal stromal tumours and related tumours in clinical practice. | Casey RT | Scientific reports | 2019 | PMID: 31308404 |
Tumour risks and genotype-phenotype correlations associated with germline variants in succinate dehydrogenase subunit genes SDHB, SDHC and SDHD. | Andrews KA | Journal of medical genetics | 2018 | PMID: 29386252 |
Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing. | Mandelker D | JAMA | 2017 | PMID: 28873162 |
Heterogeneous genetic background of the association of pheochromocytoma/paraganglioma and pituitary adenoma: results from a large patient cohort. | Dénes J | The Journal of clinical endocrinology and metabolism | 2015 | PMID: 25494863 |
Toward an improved definition of the genetic and tumor spectrum associated with SDH germ-line mutations. | Evenepoel L | Genetics in medicine : official journal of the American College of Medical Genetics | 2015 | PMID: 25394176 |
Succinate dehydrogenase (SDH)-deficient renal carcinoma: a morphologically distinct entity: a clinicopathologic series of 36 tumors from 27 patients. | Gill AJ | The American journal of surgical pathology | 2014 | PMID: 25025441 |
The clinical phenotype of SDHC-associated hereditary paraganglioma syndrome (PGL3). | Else T | The Journal of clinical endocrinology and metabolism | 2014 | PMID: 24758179 |
Succinate dehydrogenase deficiency is rare in pituitary adenomas. | Gill AJ | The American journal of surgical pathology | 2014 | PMID: 24625421 |
Germline SDHC mutation presenting as recurrent SDH deficient GIST and renal carcinoma. | Gill AJ | Pathology | 2013 | PMID: 24150194 |
Non-pheochromocytoma (PCC)/paraganglioma (PGL) tumors in patients with succinate dehydrogenase-related PCC-PGL syndromes: a clinicopathological and molecular analysis. | Papathomas TG | European journal of endocrinology | 2013 | PMID: 24096523 |
A comprehensive next generation sequencing-based genetic testing strategy to improve diagnosis of inherited pheochromocytoma and paraganglioma. | Rattenberry E | The Journal of clinical endocrinology and metabolism | 2013 | PMID: 23666964 |
Immunohistochemical loss of succinate dehydrogenase subunit A (SDHA) in gastrointestinal stromal tumors (GISTs) signals SDHA germline mutation. | Miettinen M | The American journal of surgical pathology | 2013 | PMID: 23282968 |
Imaging work-up for screening of paraganglioma and pheochromocytoma in SDHx mutation carriers: a multicenter prospective study from the PGL.EVA Investigators. | Gimenez-Roqueplo AP | The Journal of clinical endocrinology and metabolism | 2013 | PMID: 23162105 |
A decade (2001-2010) of genetic testing for pheochromocytoma and paraganglioma. | Buffet A | Hormone and metabolic research = Hormon- und Stoffwechselforschung = Hormones et metabolisme | 2012 | PMID: 22517557 |
Mutations in the heme b-binding residue of SDHC inhibit assembly of respiratory chain complex II in mammalian cells. | Lemarie A | Mitochondrion | 2009 | PMID: 19332149 |
Ligand preference and orientation in b- and c-type heme-binding proteins. | Fufezan C | Proteins | 2008 | PMID: 18491383 |
Crystal structure of mitochondrial respiratory membrane protein complex II. | Sun F | Cell | 2005 | PMID: 15989954 |
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Text-mined citations for rs786203457 ...
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.