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NM_003000.3(SDHB):c.540_540+13del

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, single submitter
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Jul 9, 2020
Accession:
VCV000468236.2
Variation ID:
468236
Description:
14bp deletion
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NM_003000.3(SDHB):c.540_540+13del

Allele ID
447493
Variant type
Deletion
Variant length
14 bp
Cytogenetic location
1p36.13
Genomic location
1: 17027736-17027749 (GRCh38) GRCh38 UCSC
1: 17354231-17354244 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_316:g.31422_31435del
NM_003000.2:c.540_540+13delGGTCATTAGTCCCT splice donor
NC_000001.10:g.17354233_17354246del
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:17027735:AGGGACTAATGACCAG:AG
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA658656888
dbSNP: rs1553177666
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Jul 14, 2017 RCV000551202.1
Likely pathogenic 1 criteria provided, single submitter Jul 9, 2020 RCV001378111.1
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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
Likely pathogenic
(Jul 14, 2017)
criteria provided, single submitter
Method: clinical testing
Paragangliomas 4
Allele origin: germline
Invitae
Accession: SCV000644761.1
Submitted: (Oct 05, 2017)
Evidence details
Comment:
This sequence change affects a donor splice site in intron 5 of the SDHB gene. It is expected to disrupt RNA splicing and likely results … (more)
Likely pathogenic
(Jul 09, 2020)
criteria provided, single submitter
Method: clinical testing
Gastrointestinal stromal tumor
Paragangliomas 4
Pheochromocytoma
Allele origin: germline
Invitae
Accession: SCV001575607.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change affects a donor splice site in intron 5 of the SDHB gene. It is expected to disrupt RNA splicing and likely results … (more)

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
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
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547

Text-mined citations for rs1553177666...

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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