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NM_003002.4(SDHD):c.242C>G (p.Pro81Arg) AND Paraganglioma

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 11, 2022
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:
RCV002251308.1

Allele description [Variation Report for NM_003002.4(SDHD):c.242C>G (p.Pro81Arg)]

NM_003002.4(SDHD):c.242C>G (p.Pro81Arg)

Gene:
SDHD:succinate dehydrogenase complex subunit D [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q23.1
Genomic location:
Preferred name:
NM_003002.4(SDHD):c.242C>G (p.Pro81Arg)
HGVS:
  • NC_000011.10:g.112088939C>G
  • NG_012337.3:g.7093C>G
  • NG_033145.1:g.2860G>C
  • NM_001276503.2:c.169+966C>G
  • NM_001276504.2:c.125C>G
  • NM_001276506.2:c.242C>G
  • NM_003002.4:c.242C>GMANE SELECT
  • NP_001263433.1:p.Pro42Arg
  • NP_001263435.1:p.Pro81Arg
  • NP_002993.1:p.Pro81Arg
  • LRG_9t1:c.242C>G
  • LRG_9:g.7093C>G
  • LRG_9p1:p.Pro81Arg
  • NC_000011.9:g.111959663C>G
  • NM_003002.2:c.242C>G
  • NR_077060.2:n.277C>G
Protein change:
P42R
Links:
dbSNP: rs80338844
NCBI 1000 Genomes Browser:
rs80338844
Molecular consequence:
  • NM_001276503.2:c.169+966C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001276504.2:c.125C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276506.2:c.242C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003002.4:c.242C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_077060.2:n.277C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Paraganglioma
Synonyms:
Carotid body tumor
Identifiers:
MONDO: MONDO:0000448; MedGen: C0030421; OMIM: PS168000; Human Phenotype Ontology: HP:0002668

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002521911Cancer Variant Interpretation Group UK, Institute of Cancer Research, London
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Mar 11, 2022) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Quantifying evidence toward pathogenicity for rare phenotypes: The case of succinate dehydrogenase genes, SDHB and SDHD.

Garrett A, Loveday C, King L, Butler S, Robinson R, Horton C, Yussuf A, Choi S, Torr B, Durkie M, Burghel GJ, Drummond J, Berry I, Wallace A, Callaway A, Eccles D, Tischkowitz M, Tatton-Brown K, Snape K, McVeigh T, Izatt L, Woodward ER, et al.

Genet Med. 2022 Jan;24(1):41-50. doi: 10.1016/j.gim.2021.08.004. Epub 2021 Nov 30.

PubMed [citation]
PMID:
34906457
PMCID:
PMC8759765

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Cancer Variant Interpretation Group UK, Institute of Cancer Research, London, SCV002521911.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)

Description

Data included in classification: Absent from gnomAD (PM2_mod) Revel score >0.7 (0.96) (PP3_sup) Within SDHD “hot region” as per Garrett et al. 2021 (https://doi.org/10.1016/j.gim.2021.08.004 (amino acid 70-114) (PM1_mod) c.242 C>T p.(Pro81Leu) identified to be pathogenic, 10 submitters, ClinVar (PM5_mod) Phenotype data: Seen in patient from UK family with right carotid body tumour diagnosed age 43y and father with carotid body paraganglioma age 60y (PP4_STR) Data not included in classification: None

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

Last Updated: Mar 5, 2024