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NM_003002.4(SDHD):c.320T>C (p.Leu107Pro) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 30, 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:
RCV002324587.3

Allele description [Variation Report for NM_003002.4(SDHD):c.320T>C (p.Leu107Pro)]

NM_003002.4(SDHD):c.320T>C (p.Leu107Pro)

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.320T>C (p.Leu107Pro)
HGVS:
  • NC_000011.10:g.112094810T>C
  • NG_012337.3:g.12964T>C
  • NM_001276503.2:c.175T>C
  • NM_001276504.2:c.203T>C
  • NM_001276506.2:c.*18T>C
  • NM_003002.4:c.320T>CMANE SELECT
  • NP_001263432.1:p.Leu59=
  • NP_001263433.1:p.Leu68Pro
  • NP_002993.1:p.Leu107Pro
  • LRG_9t1:c.320T>C
  • LRG_9:g.12964T>C
  • LRG_9p1:p.Leu107Pro
  • NC_000011.9:g.111965534T>C
  • NM_003002.2:c.320T>C
  • NR_077060.2:n.409T>C
Protein change:
L107P
Molecular consequence:
  • NM_001276506.2:c.*18T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001276504.2:c.203T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003002.4:c.320T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_077060.2:n.409T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001276503.2:c.175T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002609368Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(May 30, 2024) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Cardiac paraganglioma with a novel germline mutation of succinate dehydrogenase gene D.

Otani N, Sugano K, Inami S, Amano H, Arikawa T, Saito S, Imai K, Ushiama M, Yoshida T, Kimura N, Toyoda S, Inoue T.

Jpn J Clin Oncol. 2017 Dec 1;47(12):1193-1197. doi: 10.1093/jjco/hyx132.

PubMed [citation]
PMID:
28977582

Details of each submission

From Ambry Genetics, SCV002609368.3

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

Description

The p.L107P variant (also known as c.320T>C), located in coding exon 4 of the SDHD gene, results from a T to C substitution at nucleotide position 320. The leucine at codon 107 is replaced by proline, an amino acid with similar properties. This variant has been observed in multiple individuals with a personal and/or family history that is consistent with SDHD-associated disease (Ambry internal data). This variant was identified in a family with multiple cases of carotid body tumors (PGLs) and was shown to segregate with disease in the affected family members through the paternal line (Otani N et al. Jpn. J. Clin. Oncol., 2017 Dec;47:1193-1197). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

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

Last Updated: Aug 11, 2024