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NM_003001.5(SDHC):c.405+1G>T AND Hereditary pheochromocytoma-paraganglioma

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 5, 2024
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003996080.2

Allele description [Variation Report for NM_003001.5(SDHC):c.405+1G>T]

NM_003001.5(SDHC):c.405+1G>T

Gene:
SDHC:succinate dehydrogenase complex subunit C [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q23.3
Genomic location:
Preferred name:
NM_003001.5(SDHC):c.405+1G>T
HGVS:
  • NC_000001.11:g.161356841G>T
  • NG_012767.1:g.47466G>T
  • NG_157433.1:g.231G>T
  • NM_001035511.3:c.242-5488G>T
  • NM_001035512.3:c.303+1G>T
  • NM_001035513.3:c.246+1G>T
  • NM_001278172.3:c.140-5488G>T
  • NM_001407115.1:c.525+1G>T
  • NM_001407116.1:c.348+1G>T
  • NM_001407117.1:c.342+1G>T
  • NM_001407118.1:c.297+1G>T
  • NM_001407119.1:c.294+1G>T
  • NM_001407120.1:c.294+1G>T
  • NM_001407121.1:c.185-5488G>T
  • NM_003001.5:c.405+1G>TMANE SELECT
  • LRG_317t1:c.405+1G>T
  • LRG_317:g.47466G>T
  • NC_000001.10:g.161326631G>T
  • NM_003001.3:c.405+1G>T
Nucleotide change:
IVS5, G-T, +1
Links:
OMIM: 602413.0002; dbSNP: rs587776653
NCBI 1000 Genomes Browser:
rs587776653
Molecular consequence:
  • NM_001035511.3:c.242-5488G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001278172.3:c.140-5488G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001407121.1:c.185-5488G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001035512.3:c.303+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001035513.3:c.246+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407115.1:c.525+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407116.1:c.348+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407117.1:c.342+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407118.1:c.297+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407119.1:c.294+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407120.1:c.294+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_003001.5:c.405+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
Functional consequence:
exon loss [PubMedVariation Ontology: 0381]
Observations:
1

Condition(s)

Name:
Hereditary pheochromocytoma-paraganglioma
Synonyms:
Hereditary Paraganglioma-Pheochromocytoma Syndromes; Hereditary Paragangliomas and Pheochromocytomas
Identifiers:
MONDO: MONDO:0017366; MedGen: C1708353

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004836106All of Us Research Program, National Institutes of Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Jan 5, 2024) 		germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided108544not providedclinical testing

Citations

PubMed

Autosomal dominant malignant and catecholamine-producing paraganglioma caused by a splice donor site mutation in SDHC.

Niemann S, Müller U, Engelhardt D, Lohse P.

Hum Genet. 2003 Jul;113(1):92-4. Epub 2003 Mar 25.

PubMed [citation]
PMID:
12658451

Predictors and prevalence of paraganglioma syndrome associated with mutations of the SDHC gene.

Schiavi F, Boedeker CC, Bausch B, Peçzkowska M, Gomez CF, Strassburg T, Pawlu C, Buchta M, Salzmann M, Hoffmann MM, Berlis A, Brink I, Cybulla M, Muresan M, Walter MA, Forrer F, Välimäki M, Kawecki A, Szutkowski Z, Schipper J, Walz MK, Pigny P, et al.

JAMA. 2005 Oct 26;294(16):2057-63. Erratum in: JAMA. 2006 Feb 8;295(6):628.

PubMed [citation]
PMID:
16249420
See all PubMed Citations (7)

Details of each submission

From All of Us Research Program, National Institutes of Health, SCV004836106.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (7)

Description

This variant disrupts a canonical splice site and is predicted to result in abnormal splicing. Aberrant splicing and/or loss of function is an established mechanism of disease. This prediction has been confirmed by an mRNA study (PMID: 17667967). Different variants at the same splice site have been reported in association with disease and are independently classified as likely pathogenic or pathogenic. This variant has been reported in multiple individuals with paraganglioma (PMID: 12658451, 16249420, 22517554, 17667967, 34439371, 33748650). This variant is absent from or rare in large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown108544not providednot provided1not providednot providednot provided

Last Updated: Oct 20, 2024