NM_003002.4(SDHD):c.57del (p.Leu20fs) AND Hereditary cancer-predisposing syndrome

Clinical significance:Pathogenic (Last evaluated: Oct 3, 2015)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000492772.1

Allele description [Variation Report for NM_003002.4(SDHD):c.57del (p.Leu20fs)]

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

Gene:
SDHD:succinate dehydrogenase complex subunit D [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
11q23.1
Genomic location:
Preferred name:
NM_003002.4(SDHD):c.57del (p.Leu20fs)
HGVS:
  • NC_000011.10:g.112087861del
  • NG_012337.3:g.6015del
  • NG_033145.1:g.3938del
  • NM_001276503.2:c.57del
  • NM_001276504.2:c.52+902del
  • NM_001276506.2:c.57del
  • NM_003002.4:c.57delMANE SELECT
  • NP_001263432.1:p.Leu20fs
  • NP_001263435.1:p.Leu20fs
  • NP_002993.1:p.Leu20fs
  • LRG_9t1:c.57del
  • LRG_9:g.6015del
  • LRG_9p1:p.Leu20fs
  • NC_000011.9:g.111958585del
  • NG_012337.2:g.6015del
  • NM_003002.2:c.57del
  • NM_003002.2:c.57delG
  • NM_003002.3:c.57delG
  • NR_077060.2:n.92del
Protein change:
L20fs
Links:
OMIM: 602690.0027; dbSNP: rs587776649
NCBI 1000 Genomes Browser:
rs587776649
Molecular consequence:
  • NM_001276503.2:c.57del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001276506.2:c.57del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_003002.4:c.57del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001276504.2:c.52+902del - intron variant - [Sequence Ontology: SO:0001627]
  • NR_077060.2:n.92del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MedGen: C0027672

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000581225Ambry Geneticscriteria provided, single submitter
Pathogenic
(Oct 3, 2015)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Citations

PubMed

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, McWhinney SR, Bei T, Matyakhina L, Stergiopoulos S, Muchow M, Boikos SA, Ferrando B, Pacak K, Assie G, Baudin E, Chompret A, Ellison JW, Briere JJ, Rustin P, Gimenez-Roqueplo AP, Eng C, Carney JA, Stratakis CA.

Eur J Hum Genet. 2008 Jan;16(1):79-88. Epub 2007 Aug 1.

PubMed [citation]
PMID:
17667967

Succinate dehydrogenase gene mutations are strongly associated with paraganglioma of the organ of Zuckerkandl.

Lodish MB, Adams KT, Huynh TT, Prodanov T, Ling A, Chen C, Shusterman S, Jimenez C, Merino M, Hughes M, Cradic KW, Milosevic D, Singh RJ, Stratakis CA, Pacak K.

Endocr Relat Cancer. 2010 Jun 3;17(3):581-8. doi: 10.1677/ERC-10-0004. Print 2010 Sep.

PubMed [citation]
PMID:
20418362
PMCID:
PMC3417306
See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV000581225.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (3)

Description

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 a translational frameshift with a predicted alternate stop codon. This alteration has been previously identified in individuals with paraganglioma(s) and gastrointestinal stromal tumor (GIST) (<span style="background-color:initial">Pasini B et al. Eur. J. Hum. Genet. 2008 Jan;16(1):79-88; Lodish MB et al. Endocr. Relat. Cancer 2010 Sep;17(3):581-8; Wang YM et al. World J. Gastroenterol. 2015 Feb;21(8):2303-14).<span style="background-color:initial"> In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

Last Updated: Nov 27, 2021

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