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NM_003000.3(SDHB):c.287-1G>C AND not provided

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Oct 1, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000478921.14

Allele description [Variation Report for NM_003000.3(SDHB):c.287-1G>C]

NM_003000.3(SDHB):c.287-1G>C

Gene:
SDHB:succinate dehydrogenase complex iron sulfur subunit B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.13
Genomic location:
Preferred name:
NM_003000.3(SDHB):c.287-1G>C
HGVS:
  • NC_000001.11:g.17028737C>G
  • NG_012340.1:g.30434G>C
  • NM_001407361.1:c.287-1G>C
  • NM_003000.3:c.287-1G>CMANE SELECT
  • LRG_316t1:c.287-1G>C
  • LRG_316:g.30434G>C
  • NC_000001.10:g.17355232C>G
  • NM_003000.2:c.287-1G>C
  • c.287-1G>C
Links:
dbSNP: rs397516833
NCBI 1000 Genomes Browser:
rs397516833
Molecular consequence:
  • NM_001407361.1:c.287-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_003000.3:c.287-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
Observations:
2

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000343112Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Pathogenic
(Jun 21, 2016)
germlineclinical testing

Citation Link,

SCV000565544GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Pathogenic
(Nov 16, 2017)
germlineclinical testing

Citation Link,

SCV004123317CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Pathogenic
(Oct 1, 2023)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000343112.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000565544.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is denoted SDHB c.287-1G>C or IVS3-1G>C and consists of a G>C nucleotide substitution at the -1 position of intron 3 of the SDHB gene. This variant destroys a canonical splice acceptor site and is predicted to cause abnormal gene splicing, leading to either an abnormal message that is subject to nonsense-mediated mRNA decay or to an abnormal protein product. This variant has been reported in multiple cases with malignant paraganglioma, at least one of which showed absence of SDHB staining by immunohistochemistry (Timmers 2007, He 2009, Fishbein 2013, Jafri 2013, Sue 2015, Del Forno 2016, Gupta 2016, Jochmanova 2017). Based on currently available evidence, we consider SDHB c.287-1G>C to be a pathogenic variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV004123317.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

SDHB: PVS1, PM2

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

Last Updated: Jul 15, 2024