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NM_003002.4(SDHD):c.57del (p.Leu20fs)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Oct 22, 2021)
Last evaluated:
Jun 17, 2021
Accession:
VCV000006917.9
Variation ID:
6917
Description:
1bp deletion
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NM_003002.4(SDHD):c.57del (p.Leu20fs)

Allele ID
21956
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
11q23.1
Genomic location
11: 112087861 (GRCh38) GRCh38 UCSC
11: 111958585 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_003002.2:c.57delG
LRG_9:g.6015del
LRG_9t1:c.57del LRG_9p1:p.Leu20fs
... more HGVS
Protein change
L20fs
Other names
-
Canonical SPDI
NC_000011.10:112087860:G:
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00001
Links
ClinGen: CA016733
OMIM: 602690.0027
dbSNP: rs587776649
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 Jun 17, 2021 RCV000482313.2
Pathogenic 1 criteria provided, single submitter Oct 3, 2015 RCV000492772.1
Pathogenic 2 criteria provided, single submitter Jan 17, 2020 RCV000505302.2
Pathogenic 1 criteria provided, single submitter Oct 23, 2017 RCV000641042.1
Pathogenic 1 no assertion criteria provided Jan 1, 2008 RCV000007326.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SDHD Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
424 442

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jan 17, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary Paraganglioma-Pheochromocytoma Syndromes
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001337824.1
Submitted: (Apr 29, 2020)
Evidence details
Publications
PubMed (4)
Comment:
Variant summary: SDHD c.57delG (p.Leu20CysfsX66) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Pathogenic
(Oct 03, 2015)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000581225.4
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (3)
Comment:
The c.57delG pathogenic mutation, located in coding exon 2 of the SDHD gene, results from a deletion of one nucleotide at nucleotide position 57, causing … (more)
Pathogenic
(Jun 17, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000565548.5
Submitted: (Oct 22, 2021)
Evidence details
Comment:
Observed in individuals with a personal or family history consistent with pathogenic variants in this gene (Pasini 2008, Andrews 2018, Caetano 2021); Frameshift variant predicted … (more)
Pathogenic
(Oct 23, 2017)
criteria provided, single submitter
Method: clinical testing
Carney-Stratakis syndrome
Paragangliomas 1
Pheochromocytoma
Cowden syndrome 3
Allele origin: germline
Invitae
Accession: SCV000762660.1
Submitted: (Apr 02, 2018)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change creates a premature translational stop signal (p.Leu20Cysfs*66) in the SDHD gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Jan 01, 2008)
no assertion criteria provided
Method: literature only
PARAGANGLIOMA AND GASTRIC STROMAL SARCOMA
Allele origin: germline
OMIM
Accession: SCV000027524.4
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (2)
Pathogenic
(-)
no assertion criteria provided
Method: research
Hereditary Paraganglioma-Pheochromocytoma Syndromes
Allele origin: germline
Section on Medical Neuroendocrinolgy,National Institutes of Health
Accession: SCV000599532.1
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
Succinate dehydrogenase-deficient gastrointestinal stromal tumors. Wang YM World journal of gastroenterology 2015 PMID: 25741136
Succinate dehydrogenase gene mutations are strongly associated with paraganglioma of the organ of Zuckerkandl. Lodish MB Endocrine-related cancer 2010 PMID: 20418362
Mediastinal paragangliomas: association with mutations in the succinate dehydrogenase genes and aggressive behavior. Ghayee HK Endocrine-related cancer 2009 PMID: 19075037
Clinical and molecular genetics of patients with the Carney-Stratakis syndrome and germline mutations of the genes coding for the succinate dehydrogenase subunits SDHB, SDHC, and SDHD. Pasini B European journal of human genetics : EJHG 2008 PMID: 17667967
Familial gastrointestinal stromal tumors and germ-line mutations. McWhinney SR The New England journal of medicine 2007 PMID: 17804857

Text-mined citations for rs587776649...

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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 Dec 02, 2021