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NM_003000.2(SDHB):c.541-2A>G

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Sep 20, 2021)
Last evaluated:
Jul 9, 2021
Accession:
VCV000183925.8
Variation ID:
183925
Description:
single nucleotide variant
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NM_003000.2(SDHB):c.541-2A>G

Allele ID
181613
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p36.13
Genomic location
1: 17024076 (GRCh38) GRCh38 UCSC
1: 17350571 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_316:g.35095A>G
NC_000001.10:g.17350571T>C
NC_000001.11:g.17024076T>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:17024075:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
dbSNP: rs786201161
ClinGen: CA015950
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Apr 28, 2019 RCV000162804.3
Likely pathogenic 1 criteria provided, single submitter Jun 14, 2016 RCV000374774.2
Pathogenic 1 criteria provided, single submitter Jul 9, 2021 RCV000523104.2
Pathogenic 1 criteria provided, single submitter Aug 6, 2020 RCV000797086.3
Pathogenic 1 no assertion criteria provided - RCV000505364.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SDHB Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
789 819

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Apr 28, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000213285.6
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (3)
Comment:
The c.541-2A>G intronic pathogenic mutation results from an A to G substitution two nucleotides upstream from coding exon 6 in the SDHB gene. This mutation … (more)
Likely pathogenic
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
SDHB-Related Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000351417.2
Submitted: (Oct 18, 2016)
Evidence details
Publications
PubMed (4)
Comment:
The c.541-2A>G variant occurs in a canonical splice site (acceptor) and is therefore predicted to disrupt or distort the normal gene product. The variant has … (more)
Pathogenic
(Aug 06, 2020)
criteria provided, single submitter
Method: clinical testing
Gastrointestinal stromal tumor
Paragangliomas 4
Pheochromocytoma
Allele origin: germline
Invitae
Accession: SCV000936626.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (7)
Comment:
This sequence change affects an acceptor splice site in intron 5 of the SDHB gene. It is expected to disrupt RNA splicing and likely results … (more)
Pathogenic
(Jul 09, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000616872.2
Submitted: (Sep 20, 2021)
Evidence details
Comment:
Canonical splice site variant predicted to result in an in-frame deletion of a critical region, including the 4FE-4S ferredoxin-type domain and Iron-sulfur 2 (4Fe-4S), Iron-sulfur … (more)
Pathogenic
(-)
no assertion criteria provided
Method: research
Hereditary Paraganglioma-Pheochromocytoma Syndromes
Allele origin: germline
Section on Medical Neuroendocrinolgy,National Institutes of Health
Accession: SCV000599511.1
Submitted: (Jul 10, 2017)
Evidence details

Functional evidence

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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 this variant

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Title Author Journal Year Link
Germline SDHB and SDHD mutations in pheochromocytoma and paraganglioma patients. Huang Y Endocrine connections 2018 PMID: 30352407
Clinical and Molecular Features of Renal and Pheochromocytoma/Paraganglioma Tumor Association Syndrome (RAPTAS): Case Series and Literature Review. Casey RT The Journal of clinical endocrinology and metabolism 2017 PMID: 28973655
Magnetic resonance imaging spectrum of succinate dehydrogenase-related infantile leukoencephalopathy. Helman G Annals of neurology 2016 PMID: 26642834
SDHB-Associated Paraganglioma in a Pediatric Patient and Literature Review on Hereditary Pheochromocytoma-Paraganglioma Syndromes. Choat H Case reports in endocrinology 2014 PMID: 25298897
Succinate dehydrogenase kidney cancer: an aggressive example of the Warburg effect in cancer. Ricketts CJ The Journal of urology 2012 PMID: 23083876
Tumor risks and genotype-phenotype-proteotype analysis in 358 patients with germline mutations in SDHB and SDHD. Ricketts CJ Human mutation 2010 PMID: 19802898
The succinate dehydrogenase genetic testing in a large prospective series of patients with paragangliomas. Burnichon N The Journal of clinical endocrinology and metabolism 2009 PMID: 19454582
Clinical presentations, biochemical phenotypes, and genotype-phenotype correlations in patients with succinate dehydrogenase subunit B-associated pheochromocytomas and paragangliomas. Timmers HJ The Journal of clinical endocrinology and metabolism 2007 PMID: 17200167
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547

Text-mined citations for rs786201161...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021